cssi/SciSciGPT-SciSciNet huggingface dataset:
Meridional flows in the disk around a young star

Protoplanetary disks are known to possess a variety of substructures in the distribution of their millimetre-sized grains, predominantly seen as rings and gaps1, which are frequently interpreted as arising from the shepherding of large grains by either hidden, still-forming planets within the disk2 or (magneto-)hydrodynamic instabilities3. The velocity structure of the gas offers a unique probe of both the underlying mechanisms driving the evolution of the disk—such as movement of planet-building material from volatile-rich regions to the chemically inert midplane—and the details of the required removal of angular momentum. Here we report radial profiles of the three velocity components of gas in the upper layers of the disk of the young star HD 163296, as traced by emission from 12CO molecules. These velocities reveal substantial flows from the surface of the disk towards its midplane at the radial locations of gaps that have been argued to be opened by embedded planets4–7: these flows bear a striking resemblance to meridional flows, long predicted to occur during the early stages of planet formation8–12. In addition, a persistent radial outflow is seen at the outer edge of the disk that is potentially the base of a wind associated with previously detected extended emission12. Three-dimensional gas velocities in the gapped disk around the young star HD 163296 show meridional flows from the surface of the disk towards its midplane at gap locations.
Agency Laundering and Information Technologies

When agents insert technological systems into their decision-making processes, they can obscure moral responsibility for the results. This can give rise to a distinct moral wrong, which we call “agency laundering.” At root, agency laundering involves obfuscating one’s moral responsibility by enlisting a technology or process to take some action and letting it forestall others from demanding an account for bad outcomes that result. We argue that the concept of agency laundering helps in understanding important moral problems in a number of recent cases involving automated, or algorithmic, decision-systems. We apply our conception of agency laundering to a series of examples, including Facebook’s automated advertising suggestions, Uber’s driver interfaces, algorithmic evaluation of K-12 teachers, and risk assessment in criminal sentencing. We distinguish agency laundering from several other critiques of information technology, including the so-called “responsibility gap,” “bias laundering,” and masking.
The positive end of the polygenic score distribution for ADHD: a low risk or a protective factor?

Background Polygenic scores (PGS) are widely used to characterize genetic liability for heritable mental disorders, including attention-deficit/hyperactivity disorder (ADHD). However, little is known about the effects of a low burden of genetic liability for ADHD, including whether this functions as a low risk or protective factor for ADHD and related functional outcomes in later life. The current study examines the association of low ADHD PGS and functional outcomes in adulthood. Methods Participants were from Wave IV of the National Longitudinal Study of Adolescent to Adult Health (Add Health) (N = 7088; mean age = 29, s.d. = 1.74). ADHD PGS was computed from an existing genome-wide association study, and adult functional outcomes, including cognition, educational attainment, mental health, and physical health were assessed during in-home interviews. Results Individuals at the lowest end of the ADHD PGS distribution (i.e. lowest 20th percentile) had the lowest probabilities of ADHD, exhibiting a 17–19% reduction in risk for ADHD relative to the observed 8.3% prevalence rate of ADHD in Add Health. Furthermore, individuals with low ADHD PGS had higher cognitive performance, greater levels of educational attainment, and lower BMI relative to individuals representing the rest of the ADHD PGS distribution, including those who were in the medium and high-PGS groups. Conclusions Findings indicate that psychiatric PGS likely capture far more than just the risk and the absence of risk for a psychiatric outcome; where one lies along the PGS distribution may predict diverging functional consequences, for better and for worse.
Conditional depletion of the RNA polymerase I subunit PAF53 reveals that it is essential for mitosis and enables identification of functional domains

Our knowledge of the mechanism of rDNA transcription has benefited from the combined application of genetic and biochemical techniques in yeast. Nomura's laboratory (Nogi, Y., Vu, L., and Nomura, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 7026-7030 and Nogi, Y., Yano, R., and Nomura, M. (1991) Proc. Natl. Acad. Sci. U.S.A. 88, 3962-3966) developed a system in yeast to identify genes essential for ribosome biogenesis. Such systems have allowed investigators to determine whether a gene was essential and to determine its function in rDNA transcription. However, there are significant differences in both the structures and components of the transcription apparatus and the patterns of regulation between mammals and yeast. Thus, there are significant deficits in our understanding of mammalian rDNA transcription. We have developed a system combining CRISPR/Cas9 and an auxin-inducible degron that enables combining a "genetics-like"approach with biochemistry to study mammalian rDNA transcription. We now show that the mammalian orthologue of yeast RPA49, PAF53, is required for rDNA transcription and mitotic growth. We have studied the domains of the protein required for activity. We have found that the C-terminal, DNA-binding domain (tandem-winged helix), the heterodimerization, and the linker domain were essential. Analysis of the linker identified a putative helix-turn-helix (HTH) DNA-binding domain. This HTH constitutes a second DNA-binding domain within PAF53. The HTH of the yeast and mammalian orthologues is essential for function. In summary, we show that an auxin-dependent degron system can be used to rapidly deplete nucleolar proteins in mammalian cells, that PAF53 is necessary for rDNA transcription and cell growth, and that all three PAF53 domains are necessary for its function.
A novel hybrid modulation scheme for an isolated high-frequency-link fuel cell inverter

This paper describes a novel hybrid modulation scheme for the operation of an isolated high-frequency and high-power direct-power-conversion (DPC) inverter. It enables: (a) removal of the dc-link filter evident in conventional inverters where the diode rectifier stage is followed by low-pass filter and a voltage-source inverter (VSI); (b) significant reduction in switching loss of the inverter by modulating the switches of 2 of the 3 legs of the 6-switch ac/ac converter at 120 Hz while modulating the 3rd leg at high frequency. Unlike the VSI approach, in the DPC approach hybrid modulation enables the retention of the sine-wave modulated switching information at the output of the diode rectifier without rather than filtering it. Overall, the following is demonstrated: i) modulation scheme and uniqueness, and analytical derivation of the Fourier transformation of the output voltage; ii) derivation of a reachability condition for the DPC topology that outlines its global stability and performance; iii) demonstration of the switching and conduction losses and harmonics; and iv) scaled experimental validation. It is noted that, the term hybrid modulation has no similarity with the modulation scheme for a hybrid converter (which are conjugation of two types of converters based on a slow and fast device) reported in literature. The term hybrid modulation scheme is simply chosen because at any given time, only one leg of the inverter output stage carries out forced switching while the other two legs are not switching at all. The outlined hybrid modulation scheme is unlike all reported discontinuous modulation schemes where the input is a dc and not a pulsating modulated dc and at most only one leg stays on or off permanently in a 60° or 120° cycle.
Carcinoma of the cervix in Jewish women.

S TATISTICALLY it has been recorded on numerous occasions that there is a significantly low incidence of carcinoma of l-he cervix in dewish women. The reasons for this have been post,ulat.ed by many, but proved by none. In 1939 one of us reviewed the more important world literatureI” on this subject and published the statistics of the Mount Sinai Hospital in regard to this subject. The present paper is a ten-year follow-up of our statistics.
On the Thermal Conductivities of Single and Mixed Solids and Liquids and their Variation with Temperature

In determining thermal conductivities of solids not very good conductors of heat, the method least open to objection on theoretical grounds is the one in which a spherical shell of the substance to be tested is filled with, and the exterior surrounded by, some good conductor of heat, the temperatures of the conductors, inside and out, being observed by means of thermometers or thermo-junctions, and maintained constant by heat supplied, e. g. , electrically, to the inner conductor at a measured rate (fig. 1). Difficulties, mainly of a mechanical kind, present themselves, however, in the carrying out of this method, which render it advisable to sacrifice some of the theoretical simplicity, in order to make the method more practicable. These difficulties are overcome most easily by having the material to be tested, the conductor to which heat is supplied, and the outside conductors, in the form of flat circular discs of the same diameter (fig. 2), the good-conducting disc, C , to which heat is supplied, being placed between two discs of the material to be tested, A and B , and two other good-conducting discs, D and E , placed in contact with the outer surfaces. By placing thermo-junctions in each good-conducting disc we can determine the relation between the heat supplied to the inner disc and the differences of temperature between the inner and outer discs.
Expertise-Aware Truth Analysis and Task Allocation in Mobile Crowdsourcing

In mobile crowdsourcing, the accuracy of the collected data is usually hard to ensure. Researchers have proposed techniques to identify truth from noisy data by inferring and utilizing the reliability of mobile users, and allocate tasks to users with higher reliability. However, they neglect the fact that a user may only have expertise on some problems (in some domains), but not others, and hence causing two problems: low estimation accuracy in truth analysis and ineffective task allocation. To address these problems, we propose Expertise-aware Truth Analysis and Task Allocation ( $\mbox{ETA}^2$ ETA 2 ) , which can effectively infer user expertise, and then estimate truth and allocate tasks based on the inferred expertise. $\mbox{ETA}^2$ ETA 2 relies on a novel semantic analysis method to identify the expertise, and an expertise-aware truth analysis method to find the truth. For expertise-aware task allocation in $\mbox{ETA}^2$ ETA 2 , we formalize and solve two problems based on the optimization objectives: max-quality task allocation which maximizes the probability for tasks to be allocated to users with high expertise and min-cost task allocation which minimizes the cost of task allocation while ensuring high-quality data are collected. Experimental results based on two real-world datasets and one synthetic dataset demonstrate that $\mbox{ETA}^2$ ETA 2 significantly outperforms existing solutions.
A queue-oriented transaction processing paradigm

Transaction processing has been an active area of research for several decades. A fundamental characteristic of classical transaction processing protocols is non-determinism, which causes them to suffer from performance issues on modern computing environments such as main-memory databases using many-core, and multi-socket CPUs and distributed environments. Recent proposals of deterministic transaction processing techniques have shown great potential in addressing these performance issues. In this position paper, I argue for a queue-oriented transaction processing paradigm that leads to better design and implementation of deterministic transaction processing protocols. I support my approach with extensive experimental evaluations and demonstrate significant performance gains.
A Mirage of the Cosmic Shoreline: Venus-like Clouds as a Statistical False Positive for Exoplanet Atmospheric Erosion

Near-term studies of Venus-like atmospheres with JWST promise to advance our knowledge of terrestrial planet evolution. However, the remote study of Venus in the Solar System and the ongoing efforts to characterize gaseous exoplanets both suggest that high altitude aerosols could limit observational studies of lower atmospheres, and potentially make it challenging to recognize exoplanets as "Venus-like". To support practical approaches for exo-Venus characterization with JWST, we use Venus-like atmospheric models with self-consistent cloud formation of the seven TRAPPIST-1 exoplanets to investigate the atmospheric depth that can be probed using both transmission and emission spectroscopy. We find that JWST/MIRI LRS secondary eclipse emission spectroscopy in the 6 $\mu$m opacity window could probe at least an order of magnitude deeper pressures than transmission spectroscopy, potentially allowing access to the sub-cloud atmosphere for the two hot innermost TRAPPIST-1 planets. In addition, we identify two confounding effects of sulfuric acid aerosols that may carry strong implications for the characterization of terrestrial exoplanets with transmission spectroscopy: (1) there exists an ambiguity between cloud-top and solid surface in producing the observed spectral continuum; and (2) the cloud-forming region drops in altitude with semi-major axis, causing an increase in the observable cloud-top pressure with decreasing stellar insolation. Taken together, these effects could produce a trend of thicker atmospheres observed at lower stellar insolation---a convincing false positive for atmospheric escape and an empirical "cosmic shoreline". However, developing observational and theoretical techniques to identify Venus-like exoplanets and discriminate them from stellar windswept worlds will enable advances in the emerging field of terrestrial comparative planetology.
Breaking the far-field diffraction limit in optical nanopatterning via repeated photochemical and electrochemical transitions in photochromic molecules.

By saturating a photochromic transition with a nodal illumination (wavelength, $\ensuremath{\lambda}$), one isomeric form of a small molecule is spatially localized to a region smaller than the far-field diffraction limit. A selective oxidation step effectively locks this pattern allowing repeated patterning. Using this approach and a two-beam interferometer, we demonstrate isolated lines as narrow as $\ensuremath{\lambda}/8$ (78 nm) and spacing between features as narrow as $\ensuremath{\lambda}/4$ (153 nm). This is considerably smaller than the minimum far-field diffraction limit of $\ensuremath{\lambda}/2$. Most significantly, nanopatterning is achieved via single-photon reactions and at low light levels, which in turn allow for high throughput.
Aversive Learning Increases Release Probability of Olfactory Sensory Neurons

Predicting danger from previously associated sensory stimuli is essential for survival. Contributions from altered peripheral sensory inputs are implicated in this process, but the underlying mechanisms remain elusive. Here, we use the mammalian olfactory system to investigate such mechanisms. Primary olfactory sensory neurons (OSNs) project their axons directly to the olfactory bulb (OB) glomeruli, where their synaptic release is subject to local and cortical influence and neuromodulation. Pairing optogenetic activation of a single glomerulus with foot shock in mice induces freezing to light stimulation alone during fear retrieval. This is accompanied by an increase in OSN release probability and a reduction in GABAB receptor expression in the conditioned glomerulus. Furthermore, freezing time is positively correlated with the release probability of OSNs in fear-conditioned mice. These results suggest that aversive learning increases peripheral olfactory inputs at the first synapse, which may contribute to the behavioral outcome.
P2X1 Selective Antagonists Block HIV-1 Infection through Inhibition of Envelope Conformation-Dependent Fusion.

Purinergic receptors are well-established modulators of inflammatory processes, primarily through detection of extracellular nucleotides that are released by dying or infected cells. Emerging literature has demonstrated that inhibition of these inflammatory receptors can block HIV-1 productive infection and HIV-1-associated inflammation. The specificity of receptor type and mechanism of interaction has not yet been determined. Here, we characterize the inhibitory activity of P2X1 receptor antagonists, NF279 and NF449, in cell lines, primary cells, and a variety of HIV-1 envelope (Env) clades. NF279 and NF449 blocked productive infection at the level of viral membrane fusion, with a range of inhibitory activities against different HIV-1 Env isolates. A mutant virus carrying a truncation deletion of the C-terminal tail of HIV-1 Env glycoprotein 41 (gp41) showed reduced sensitivity to P2X1 antagonists, indicating that the sensitivity of inhibition by these molecules may be modulated by Env conformation. In contrast, a P2X7 antagonist, A438079, had a limited effect on productive infection and fusion. NF279 and NF449 interfered with the ability of the gp120 variable regions 1 and 2 (V1V2)-targeted broadly neutralizing antibody PG9 to block productive infection, suggesting that these drugs may antagonize HIV-1 Env at gp120 V1V2 to block viral membrane fusion. Our observations indicate that P2X1 antagonism can inhibit HIV-1 replication at the level of viral membrane fusion through interaction with Env. Future studies will probe the nature of these compounds in inhibiting HIV-1 fusion and the development of small molecules to block HIV-1 entry via this mechanism. IMPORTANCE While effective treatment can lower the severe morbidity and mortality associated with HIV-1 infection, patients infected with HIV-1 suffer from significantly higher rates of noncommunicable comorbidities associated with chronic inflammation. Emerging literature suggests a key role for P2X1 receptors in mediating this chronic inflammation, but the mechanism is still unknown. Here, we demonstrate that HIV-1 infection is reduced by P2X1 receptor antagonism. This inhibition is mediated by interference with HIV-1 Env and can impact a variety of viral clades. These observations highlight the importance of P2X1 antagonists as potential novel therapeutics that could serve to block a variety of different viral clades with additional benefits for their anti-inflammatory properties.
Quantitative Genomic Dissection of Soybean Yield Components

Soybean is a crop of major economic importance with low rates of genetic gains for grain yield compared to other field crops. A deeper understanding of the genetic architecture of yield components may enable better ways to tackle the breeding challenges. Key yield components include the total number of pods, nodes and the ratio pods per node. We evaluated the SoyNAM population, containing approximately 5600 lines from 40 biparental families that share a common parent, in 6 environments distributed across 3 years. The study indicates that the yield components under evaluation have low heritability, a reasonable amount of epistatic control, and partially oligogenic architecture: 18 quantitative trait loci were identified across the three yield components using multi-approach signal detection. Genetic correlation between yield and yield components was highly variable from family-to-family, ranging from -0.2 to 0.5. The genotype-by-environment correlation of yield components ranged from -0.1 to 0.4 within families. The number of pods can be utilized for indirect selection of yield. The selection of soybean for enhanced yield components can be successfully performed via genomic prediction, but the challenging data collections necessary to recalibrate models over time makes the introgression of QTL a potentially more feasible breeding strategy. The genomic prediction of yield components was relatively accurate across families, but less accurate predictions were obtained from within family predictions and predicting families not observed included in the calibration set.
Formation of Tidal Captures and Gravitational Wave Inspirals in Binary-Single Interactions

We perform the first systematic study on how dynamical stellar tides and general relativistic (GR) effects affect the dynamics and outcomes of binary-single interactions. For this, we have constructed an N-body code that includes tides in the affine approximation, where stars are modeled as self-similar ellipsoidal polytropes, and GR corrections using the commonly-used post-Newtonian formalism. Using this numerical formalism, we are able resolve the leading effect from tides and GR across several orders of magnitude in both stellar radius and initial target binary separation. We find that the main effect from tides is the formation of two-body tidal captures that form during the chaotic and resonant evolution of the triple system. The two stars undergoing the capture spiral in and merge. The inclusion of tides can thus lead to an increase on the stellar coalescence rate. We also develop an analytical framework for calculating the cross section of tidal inspirals between any pair of objects with similar mass. From our analytical and numerical estimates we find that the rate of tidal inspirals relative to collisions increases as the initial semi-major axis of the target binary increases and the radius of the interacting tidal objects decreases. The largest effect is therefore found for triple systems hosting white dwarfs and neutron stars. In this case, we find the rate of highly eccentric white dwarf - neutron star mergers to likely be dominated by tidal inspirals. While tidal inspirals occur rarely, we note that they can give rise to a plethora of thermonuclear transients such as Ca-rich transients.
Induced Charge Anisotropy: A Hidden Variable Affecting Ion Transport through Membranes

Summary The ability of semipermeable membranes to selectively impede the transport of undesirable solutes is key to many applications. Yet obtaining a systematic understanding of how membrane structure affects selectivity remains elusive due to the insufficient spatiotemporal resolution of existing experimental techniques and the inaccessibility of relevant solute transport timescales to conventional molecular simulations. Here, we utilize jumpy forward-flux sampling to probe the transport of sodium and chloride ions through a graphitic membrane with sub-nanometer pores. We find chlorides to traverse the pore at rates over two orders of magnitude faster than sodiums. We also identify two major impediments to the transport of both ion types. In addition to the partial dehydration of the leading ion, its traversal induces charge anisotropy at its rear, which exerts a net restraining force on the ion. Charge anisotropy is therefore a crucial hidden variable controlling the kinetics of ion transport through nanopores.
Pulsar gamma-rays: Spectra luminosities and efficiencies

The general characteristics of pulsar gamma ray spectra are presented for a model where the gamma rays are produced by curvature radiation from energetic particles above the polar cap and attenuated by pair production. The shape of the spectrum is found to depend on pulsar period, magnetic field strength, and primary particle energy. By a comparison of numerically calculated spectra with the observed spectra of the Crab and Vela pulsars, it is determined that primary particles must be accelerated to energies of about 3 x 10 to the 7th power mc sq. A genaral formula for pulsar gamma ray luminosity is determined and is found to depend on period and field strength.
Mutational load and the functional fraction of the human genome.

The fraction of the human genome that is functional is a question of both evolutionary and practical importance. Studies of sequence divergence have suggested that the functional fraction of the human genome is likely to be no more than ∼15%. In contrast, the ENCODE project, a systematic effort to map regions of transcription, transcription factor association, chromatin structure, and histone modification, assigned function to 80% of the human genome. In this article, we examine whether and how an analysis based on mutational load might set a limit on the functional fraction. In order to do so, we characterize the distribution of fitness of a large, finite, diploid population at mutation-selection equilibrium. In particular, if mean fitness is ∼1, the fitness of the fittest individual likely to occur cannot be unreasonably high. We find that at equilibrium, the distribution of log fitness has variance nus, where u is the per-base deleterious mutation rate, n is the number of functional sites (and hence incorporates the functional fraction f), and s is the selection coefficient of deleterious mutations. In a large (N=109) reproducing population, the fitness of the fittest individual likely to exist is ∼e5nus. These results apply to both additive and recessive fitness schemes. Our approach is different from previous work that compared mean fitness at mutation-selection equilibrium with the fitness of an individual who has no deleterious mutations; we show that such an individual is exceedingly unlikely to exist. We find that the functional fraction is not very likely to be limited substantially by mutational load, and that any such limit, if it exists, depends strongly on the selection coefficients of new deleterious mutations.
Estimating stochastic linear combination of non-linear regressions efficiently and scalably

Abstract Recently, many machine learning and statistical models such as non-linear regressions, the Single Index, Multi-index, Varying Coefficient Index Models and Two-layer Neural Networks can be reduced to or be seen as a special case of a new model which is called the Stochastic Linear Combination of Non-linear Regressions model. However, due to the high non-convexity of the problem, there is no previous work study how to estimate the model. In this paper, we provide the first study on how to estimate the model efficiently and scalably. Specifically, we first show that with some mild assumptions, if the variate vector x is multivariate Gaussian, then there is an algorithm whose output vectors have l2-norm estimation errors of O ( p n ) with high probability, where p is the dimension of x and n is the number of samples. The key idea of the proof is based on an observation motived by the Stein’s lemma. Then we extend our result to the case where x is bounded and sub-Gaussian using the zero-bias transformation, which could be seen as a generalization of the classic Stein’s lemma. We also show that with some additional assumptions there is an algorithm whose output vectors have l∞-norm estimation errors of O ( 1 p + p n ) with high probability. We also provide a concrete example to show that there exists some link function which satisfies the previous assumptions. Finally, for both Gaussian and sub-Gaussian cases we propose a faster sub-sampling based algorithm and show that when the sub-sample sizes are large enough then the estimation errors will not be sacrificed by too much. Experiments for both cases support our theoretical results. To the best of our knowledge, this is the first work that studies and provides theoretical guarantees for the stochastic linear combination of non-linear regressions model.
Rathat: A self-targeting printable brain implant system

There has not been a major change in how neuroscientists approach stereotaxic methods in decades. Here, we present a new stereotaxic method that provides an alternative approach to a traditional u-frame stereotaxic device and reduces costs, surgical time, and aids repeatability. The RatHat brain implantation system is a 3D-printable stereotaxic device for rats that is fabricated prior to surgery and fits to the shape of the skull. RatHat builds are directly implanted into the brain without the need for head-leveling or coordinate-mapping during surgery. The RatHat can be used in conjunction with the traditional u-frame stereotaxic device, but does not require the use of a micromanipulator for successful implantations. Each RatHat contains several primary components including the implant for mounting intracranial components, the surgical stencil for targeting drill sites, and the protective cap for preventing damage from impacts and debris. Each component serves a unique function and can be used together or separately. We demonstrate the feasibility of the RatHat in four different proof-of-principle experiments: (1) a three-pole cannula apparatus, (2) an optrode-electrode assembly, (3) a fixed-electrode array, and (4) a tetrode hyperdrive. Implants were successful, durable, and long-lasting (up to nine months). RatHat print files are easily created, can be modified in computer aided design (CAD) software for a variety of applications, and are easily shared, contributing to open science goals and replications. The RatHat has been adapted to multiple experimental paradigms in our lab and should be a useful new way to conduct stereotaxic implant surgeries in rodents.
Face Phylogeny Tree Using Basis Functions

Photometric transformations, such as brightness and contrast adjustment, can be applied to a face image repeatedly resulting in a set of near-duplicate images. Identifying the original image from a set of such near-duplicates and deducing the relationship between them are important in the context of digital image forensics. This is commonly done by generating an image phylogeny tree (IPT)—a hierarchical structure depicting the relationship between a set of near-duplicate images. In this work, we utilize three different families of basis functions to model pairwise relationships between near-duplicate images. The basis functions used in this work are orthogonal polynomials, wavelet basis functions and radial basis functions. We perform extensive experiments to assess the performance of the proposed method across three different modalities, namely, face, fingerprint and iris; across different image phylogeny tree configurations; and across different types of photometric transformations. We also utilize the same basis functions to model geometric transformations and deep-learning based transformations. Finally, we utilize the concept of approximate von Neumann graph entropy to explain the success and failure cases of the proposed IPT generation algorithm. Experiments indicate that the proposed algorithm generalizes well across different scenarios thereby suggesting the merits of using basis functions to model the relationship between photometrically or geometrically modified images.
Using multiple reference genomes to identify and resolve annotation inconsistencies.

Advances in sequencing technologies have led to the release of reference genomes and annotations for multiple individuals within more well-studied systems. While each of these new genome assemblies shares significant portions of synteny between each other, the annotated structure of gene models within these regions can differ. Of particular concern are split-gene misannotations, in which a single gene is incorrectly annotated as two distinct genes or two genes are incorrectly annotated as a single gene. These misannotations can have major impacts on functional prediction, estimates of expression, and many downstream analyses. We developed a high-throughput method based on pairwise comparisons of annotations that detect potential split-gene misannotations and quantifies support for whether the genes should be merged into a single gene model. We demonstrated the utility of our method using gene annotations of three reference genomes from maize (B73, PH207, and W22), a difficult system from an annotation perspective due to the size and complexity of the genome. On average, we found several hundred of these potential split-gene misannotations in each pairwise comparison, corresponding to 3–5% of gene models across annotations. To determine which state (i.e. one gene or multiple genes) is biologically supported, we utilized RNAseq data from 10 tissues throughout development along with a novel metric and simulation framework. The methods we have developed require minimal human interaction and can be applied to future assemblies to aid in annotation efforts. Split-gene misannotations occur at appreciable frequency in maize annotations. We have developed a method to easily identify and correct these misannotations. Importantly, this method is generic in that it can utilize any type of short-read expression data. Failure to account for split-gene misannotations has serious consequences for biological inference, particularly for expression-based analyses.
Some majorization inequalities induced by Schur products in Euclidean Jordan algebras

Abstract In a Euclidean Jordan algebra V of rank n, an element x is said to be majorized by an element y, symbolically x ≺ y , if the corresponding eigenvalue vector λ ( x ) is majorized by λ ( y ) in R n . In this article, we describe pointwise majorization inequalities of the form T ( x ) ≺ S ( x ) , where T and S are linear transformations induced by Schur products. Specializing, we recover analogs of majorization inequalities of Schur, Hadamard, and Oppenheimer stated in the setting of Euclidean Jordan algebras, as well as majorization inequalities connecting quadratic and Lyapunov transformations on V . We also show how Schur products induced by certain scalar means (such as arithmetic, geometric, harmonic, and logarithmic means) naturally lead to majorization inequalities.
Reconciling the observed mid-depth exponential ocean stratification with weak interior mixing and Southern Ocean dynamics via boundary-intensified mixing

Munk (Deep Sea Res Oceanogr Abstr 13(4):707–730, 1966) showed that the mid-depth (1–3 km) vertical temperature profile is consistent with a one-dimensional vertical advection–diffusion balance, with a constant upwelling and an interior diapycnal diffusivity of $${\mathcal {O}}(10^{-4})\,\hbox {m}^{2}\,\hbox {s}^{-1}$$. However, typical observed diffusivities in the interior are $${\mathcal {O}}(10^{-5})\,\hbox {m}^{2}\,\hbox {s}^{-1}$$. Recent work suggested that the mid-depth stratification is set by Southern Ocean (SO) isopycnal slopes, governed by SO wind and eddies, that communicate the surface outcrop positions to the mid-depth ocean. It is shown here, using an idealized ocean general circulation model, that while SO dynamics play an important role by linking the surface water mass transformation by air-sea fluxes with the mid-depth interior stratification, they do not set the observed exponential stratification and that interior mixing must contribute. Strong diapycnal mixing concentrated near the ocean boundaries is shown to be balanced locally by upwelling. A one-dimensional Munk-like balance in these boundary-mixing areas, although with much larger mixing and upwelling, leads to an exponential mid-depth temperature stratification, which spreads via isopycnal advection and mixing to the ocean interior. The exponential profile is robust to vertical variations in the vertical velocity and persists despite the observed weak interior diapycnal mixing. These results may suggest a way to reconcile the observed exponential interior mid-depth temperature stratification, the weak diapycnal diffusivity observed in tracer release experiments, and the role of Southern Ocean dynamics.
Undecidability, unit groups, and some totally imaginary infinite extensions of $\mathbb {Q}$

We produce new examples of totally imaginary infinite extensions of $\mathbb{Q}$ which have undecidable first-order theory by generalizing the methods used by Martinez-Ranero, Utreras and Videla for $\mathbb{Q}^{(2)}$. In particular, we use parametrized families of polynomials whose roots are totally real units to apply methods originally developed to prove the undecidability of totally real fields. This proves the undecidability of $\mathbb{Q}^{(d)}_{ab}$ for all $d \geq 2$.
Perioperative considerations in nonagenarians.

Objective The nation's aging population presents novel perioperative challenges. Potential benefits of operative interventions must be scrutinized in relation to recoverable quality of life. The purpose of this study is to evaluate common risk calculators used for medical decision making in a nonagenarian patient population. Methods Retrospective medical record review was performed on patients 90 years or older who underwent operative interventions requiring anesthesia at a large academic medical center between January 1, 2013, and December 31, 2017. GraphPad 8.2.1 was used for statistical analysis. Results Significant differences were found when data were stratified by age for elective versus emergent cases (P value < .0001), ability to return to baseline function (P value = .0062), and mortality (P value < .0001). Significant differences were found in emergent and elective cases, ability to return to baseline function, readmissions, and mortality (all P values < .0001) when stratified by American Society of Anesthesiologists score. Ability of patients to return to baseline functionality after intervention was influenced by their preintervention level of functionality (P value = .0008). American College of Surgeons and Portsmouth Physiologic and Operative Severity Score for Enumeration of Mortality and Morbidity risk calculators underestimated the need for rehabilitation and overestimated mortality for this population (all P values < .0001). Conclusion Perioperative cares of the extreme geriatric population are complex and should be approached collaboratively. Rehabilitation and postoperative assistance resources should be assessed and used fully. Input from palliative care teams should be sought appropriately. End-of-life and escalation-of-care discussions should ideally be organized prior to emergent interventions. Frailty and risk calculators should be used and considered for formal implementation into the preoperative workflow.
6 – Quadratic Equations

Publisher Summary This chapter discusses quadratic equations. A new method of solving quadratic equations has been developed; this new method is called “completing the square.” Completing the square on a quadratic equation allows obtaining the solutions, regardless of whether the equation can be factored. The key to understanding the method of completing the square lies in recognizing the relationship between the last two terms of any perfect square trinomial whose leading coefficient is 1. The quadratic formula is a useful tool in mathematics. It allows solving all types of quadratic equations. The chapter describes the discriminant, which is used to find the kind of solutions a quadratic equation has without solving the equation. The zero-factor property is used to build equations from their solutions. The zero-factor property and long division with polynomials are used to solve some third-degree equations. The quadratic formula gives the solutions to any quadratic equation in standard form.
Automatic repair of convex optimization problems

Given an infeasible, unbounded, or pathological convex optimization problem, a natural question to ask is: what is the smallest change we can make to the problem’s parameters such that the problem becomes solvable? In this paper, we address this question by posing it as an optimization problem involving the minimization of a convex regularization function of the parameters, subject to the constraint that the parameters result in a solvable problem. We propose a heuristic for approximately solving this problem that is based on the penalty method and leverages recently developed methods that can efficiently evaluate the derivative of the solution of a convex cone program with respect to its parameters. We illustrate our method by applying it to examples in optimal control and economics.
Molecular taxonomy of human ocular outflow tissues defined by single-cell transcriptomics

The conventional outflow pathway is a complex tissue responsible for maintaining intraocular pressure (IOP) homeostasis. The coordinated effort of multiple cells with differing responsibilities ensures healthy outflow function and IOP maintenance. Dysfunction of one or more resident cell types results in ocular hypertension and risk for glaucoma, a leading cause of blindness. In this study, single-cell RNA sequencing was performed to generate a comprehensive cell atlas of human conventional outflow tissues. We obtained expression profiles of 17,757 genes from 8,758 cells from eight eyes of human donors representing the outflow cell transcriptome. Upon clustering analysis, 12 distinct cell types were identified, and region-specific expression of candidate genes was mapped in human tissues. Significantly, we identified two distinct expression patterns (myofibroblast- and fibroblast-like) from cells located in the trabecular meshwork (TM), the primary structural component of the conventional outflow pathway. We also located Schwann cell and macrophage signatures in the TM. The second primary component structure, Schlemm's canal, displayed a unique combination of lymphatic/blood vascular gene expression. Other expression clusters corresponded to cells from neighboring tissues, predominantly in the ciliary muscle/scleral spur, which together correspond to the uveoscleral outflow pathway. Importantly, the utility of our atlas was demonstrated by mapping glaucoma-relevant genes to outflow cell clusters. Our study provides a comprehensive molecular and cellular classification of conventional and unconventional outflow pathway structures responsible for IOP homeostasis.
Real Exchange Rate Overshooting in Large Depreciations: Determinants and Consequences

The consequences of large depreciations on economic activity depend on the relative strength of the contractionary balance sheet and expansionary expenditure switching effects. However, the two operate over different time horizons: the balance sheet effect hits almost immediately, while expenditure switching is delayed by nominal rigidities and other frictions. The paper hypothesizes that the overshooting phase—observed early in the depreciation episode and driven by the balance sheet effect—is largely irrelevant for expenditure switching, which is more closely aligned with ex-post equilibrium depreciation. Given this, larger real exchange rate overshooting should signal a relatively stronger balance sheet effect. Empirical findings support this hypothesis: (i) overshooting is driven by factors associated with the balance sheet effect (high external debt, low reserves, low trade openness), (ii) overshooting-based measures of the balance sheet effect foreshadow post-depreciation output losses, and (iii) the balance sheet effect is strongest early on, while expenditure switching strengthens over the medium term.
Why were interest-only mortgages so popular during the U.S. housing boom?

Abstract Borrowers in U.S. cities where house prices boomed in the 2000s relied heavily on backloaded interest-only (IO) mortgages that require borrowers to only pay interest for the first few years of the loan. We develop a theory that encompasses common explanations for IO use, and show that while they can account for much of the regional variation in IOs, they cannot explain why IOs were popular in boom cities. We propose a new explanation. In our model, uncertain price appreciation coupled with non-recourse lending can lead to speculation financed with backloaded mortgages. We find evidence that IO borrowers behaved in ways consistent with such speculation, and discuss the policy implications of our findings.
Phonetic and Visual Priors for Decipherment of Informal Romanization

Informal romanization is an idiosyncratic process used by humans in informal digital communication to encode non-Latin script languages into Latin character sets found on common keyboards. Character substitution choices differ between users but have been shown to be governed by the same main principles observed across a variety of languages—namely, character pairs are often associated through phonetic or visual similarity. We propose a noisy-channel WFST cascade model for deciphering the original non-Latin script from observed romanized text in an unsupervised fashion. We train our model directly on romanized data from two languages: Egyptian Arabic and Russian. We demonstrate that adding inductive bias through phonetic and visual priors on character mappings substantially improves the model’s performance on both languages, yielding results much closer to the supervised skyline. Finally, we introduce a new dataset of romanized Russian, collected from a Russian social network website and partially annotated for our experiments.
A Transductive Approach for Video Object Segmentation

Semi-supervised video object segmentation aims to separate a target object from a video sequence, given the mask in the first frame. Most of current prevailing methods utilize information from additional modules trained in other domains like optical flow and instance segmentation, and as a result they do not compete with other methods on common ground. To address this issue, we propose a simple yet strong transductive method, in which additional modules, datasets, and dedicated architectural designs are not needed. Our method takes a label propagation approach where pixel labels are passed forward based on feature similarity in an embedding space. Different from other propagation methods, ours diffuses temporal information in a holistic manner which take accounts of long-term object appearance. In addition, our method requires few additional computational overhead, and runs at a fast ~37 fps speed. Our single model with a vanilla ResNet50 backbone achieves an overall score of 72.3% on the DAVIS 2017 validation set and 63.1% on the test set. This simple yet high performing and efficient method can serve as a solid baseline that facilitates future research. Code and models are available at https://github.com/ microsoft/transductive-vos.pytorch.
Resolvent degree, Hilbert’s 13th Problem and geometry

We develop the theory of resolvent degree, introduced by Brauer \cite{Br} in order to study the complexity of formulas for roots of polynomials and to give a precise formulation of Hilbert's 13th Problem. We extend the context of this theory to enumerative problems in algebraic geometry, and consider it as an intrinsic invariant of a finite group. As one application of this point of view, we prove that Hilbert's 13th Problem, and his Sextic and Octic Conjectures, are equivalent to various enumerative geometry problems, for example problems of finding lines on a smooth cubic surface or bitangents on a smooth planar quartic.
HAT: Hardware-Aware Transformers for Efficient Natural Language Processing

Transformers are ubiquitous in Natural Language Processing (NLP) tasks, but they are difficult to be deployed on hardware due to the intensive computation. To enable low-latency inference on resource-constrained hardware platforms, we propose to design Hardware-Aware Transformers (HAT) with neural architecture search. We first construct a large design space with arbitrary encoder-decoder attention and heterogeneous layers. Then we train a SuperTransformer that covers all candidates in the design space, and efficiently produces many SubTransformers with weight sharing. Finally, we perform an evolutionary search with a hardware latency constraint to find a specialized SubTransformer dedicated to run fast on the target hardware. Extensive experiments on four machine translation tasks demonstrate that HAT can discover efficient models for different hardware (CPU, GPU, IoT device). When running WMT’14 translation task on Raspberry Pi-4, HAT can achieve 3× speedup, 3.7× smaller size over baseline Transformer; 2.7× speedup, 3.6× smaller size over Evolved Transformer with 12,041× less search cost and no performance loss. HAT is open-sourced at https://github.com/mit-han-lab/hardware-aware-transformers.