cssi/SciSciGPT-SciSciNet huggingface dataset:
High-resolution transcriptional and morphogenetic profiling of cells from micropatterned human embryonic stem cell gastruloid cultures

Summary During mammalian gastrulation, germ layers arise and are shaped into the body plan while extraembryonic layers sustain the embryo. Human embryonic stem cells, cultured with BMP4 on extracellular matrix micro-discs, reproducibly differentiate into gastruloids, expressing markers of germ layers and extraembryonic cells with radial organization. Single-cell RNA sequencing and cross-species comparisons with mouse and cynomolgus monkey gastrulae suggest that gastruloids contain seven major cell types, including epiblast, ectoderm, mesoderm, endoderm, and extraembryonic trophoblast- and amnion-like cells. Upon gastruloid dissociation, single cells reseeded onto micro-discs were motile and aggregated with the same but segregated from distinct cell types. Ectodermal cells segregated from endodermal and extraembryonic cells but mixed with mesodermal cells. Our work demonstrates that the gastruloid system supports primate-specific features of embryogenesis, and that gastruloid cells exhibit evolutionarily conserved sorting behaviors. This work generates a resource for transcriptomes of human extraembryonic and embryonic germ layers differentiated in a stereotyped arrangement.
Inverse Optimal Planning for Air Traffic Control

We envision a system that concisely describes the rules of air traffic control, assists human operators and supports dense autonomous air traffic around commercial airports. We develop a method to learn the rules of air traffic control from real data as a cost function via maximum entropy inverse reinforcement learning. This cost function is used as a penalty for a search-based motion planning method that discretizes both the control and the state space. We illustrate the methodology by showing that our approach can learn to imitate the airport arrival routes and separation rules of dense commercial air traffic. The resulting trajectories are shown to be safe, feasible, and efficient.
Effects of trap confinement on personality measurements in two terrestrial rodents.

In recent years, consistent individual differences in behavior, or personalities, have been a topic of increasing interest as researchers strive to understand and predict the responses of individuals and populations to anthropogenic changes. Behavioral studies in wild populations often require that animals are live trapped before behavioral observation can occur, and this is especially true in studies investigating animal personalities. However, it is unknown whether the amount of time confined to a live trap may regulate the behavior of trapped individuals. Specifically, if the duration of trap confinement directly influences behavior, then by obtaining wild animals through live trapping we may be confounding the very measurements of greatest interest. To investigate whether the duration of trap confinement influences the behavior of trapped individuals, we performed a study on two small mammal species, focusing specifically on personality traits. We positioned high-definition trail cameras facing Longworth small mammal traps in the field to observe capture events and record the time of capture. We then measured personality in captured deer mice (Peromyscus maniculatus) and southern red-backed voles (Myodes gapperi) using three standardized tests, and through linear and generalized linear models we found that the time an animal had spent confined to a trap before testing did not affect 86% of behaviors exhibited. Our results showed two weak behavioral effects of confinement duration on boldness and docility resulting from an interaction between the duration of confinement and whether or not an individual was naive to trapping. Our results suggest that behavioral measurements of wild, trapped small mammals are not determined by the time spent confined to a trap. However, researchers should use caution and consider whether an animal is naive to trapping during analysis since habituation to the live trap may play a role in the effects of confinement duration on behavior.
Real-Time Charge Initialization of Diamond Nitrogen-Vacancy Centers for Enhanced Spin Readout

Spin qubits based on nitrogen-vacancy centers in diamond are useful only when the defect exists in the correct charge state---but this state is usually uncontrolled, since it is sensitive to the optical fields used to interrogate the qubit. Using fast, real-time photon detection and control, the authors deterministically prepare the desired charge state and demonstrate that the qubit's performance as a magnetic sensor is dramatically improved. These experiments yield deeper understanding of the charge and spin dynamics of N-$V$ centers, and the all-optical method can be adapted to dynamically control other stochastic properties of solid-state defects for improved performance.
A classical proof that the algebraic homotopy class of a rational function is the residue pairing

Abstract Cazanave has identified the algebraic homotopy class of a rational function of 1 variable with an explicit nondegenerate symmetric bilinear form. Here we show that Hurwitz's proof of a classical result about real rational functions essentially gives an alternative proof of the stable part of Cazanave's result. We also explain how this result can be interpreted in terms of the residue pairing and that this interpretation relates the result to the signature theorem of Eisenbud, Khimshiashvili, and Levine, showing that Cazanave's result answers a question posed by Eisenbud for polynomial functions in 1 variable. Finally, we announce results answering this question for functions in an arbitrary number of variables.
Plasmon enhanced second harmonic generation by periodic arrays of triangular nanoholes coupled to quantum emitters

Optical properties of periodic arrays of nanoholes of a triangular shape with experimentally realizable parameters are examined in both linear and nonlinear regimes. By utilizing a fully vectorial three-dimensional approach based on the nonlinear hydrodynamic Drude model describing metal coupled to Maxwell's equations and Bloch equations for molecular emitters, we analyze linear transmission, reflection, and nonlinear power spectra. Rigorous numerical calculations demonstrating second and third harmonic generation by the triangular hole arrays are performed. It is shown that both the Coulomb interaction of conduction electrons and the convective term contribute on equal footing to the nonlinear response of metal. It is demonstrated that the energy conversion efficiency in the second harmonic process is the highest when the system is pumped at the localized surface plasmon resonance. When molecular emitters are placed on a surface of the hole array line shapes, the second harmonic signal exhibits three peaks corresponding to second harmonics of the localized surface plasmon mode and upper and lower polaritonic states.
Models for Understanding Divergent Reactivity in Lewis Acid-Catalyzed Transformations of Carbonyls and Olefins

Carbonyl–ene, Prins, and carbonyl–olefin metathesis reactions represent powerful strategies for carbon–carbon bond formation relying on Lewis acid catalysts. Although common Lewis acids are able to...
Classifying fusion categories $$\otimes $$⊗-generated by an object of small Frobenius–Perron dimension

The goal of this paper is to classify fusion categories $${\mathcal {C}}$$ which are $$\otimes $$-generated by an object X of Frobenius–Perron dimension less than 2, with the additional mild assumption that the adjoint subcategory of $${\mathcal {C}}$$ is $$\otimes $$-generated by the object $$X\otimes X^*$$. This classification has recently become accessible due to a result of Morrison and Snyder, showing that any such category must be a cyclic extension of a category of adjoint ADE type. Our main tools in this classification are the results of Etingof et al. (Quantum Topol 1(3);209–273, 2010. https://doi.org/10.4171/QT/6), classifying cyclic extensions of a given category in terms of data computed from the Brauer–Picard group, and Drinfeld centre of that category, and the results of Edie-Michell (Int. J. Math. 29(5):1850036, 2018. https://doi.org/10.1142/S0129167X18500362) which compute the Brauer–Picard group and Drinfeld centres of the categories of adjoint ADE type. Our classification includes the expected categories, constructed from cyclic groups and the categories of ADE type. More interestingly we have categories in our classification that are non-trivial de-equivariantizations of these expected categories. Most interesting of all, our classification includes three infinite families constructed from the exceptional quantum subgroups $${\mathcal {E}}_4$$ of $${\mathcal {C}}( \mathfrak {sl}_4, 4)$$, and $${\mathcal {E}}_{16,6}$$ of $${\mathcal {C}}( \mathfrak {sl}_2, 16)\boxtimes {\mathcal {C}}( \mathfrak {sl}_3,6)$$.
The RNA-binding protein DAZL functions as repressor and activator of mRNA translation during oocyte maturation.

Deleted in azoospermia-like (DAZL) is an RNA-binding protein critical for gamete development. In full-grown oocytes, the DAZL protein increases 4-fold during reentry into the meiotic cell cycle. Here, we have investigated the functional significance of this accumulation at a genome-wide level. Depletion of DAZL causes a block in maturation and widespread disruption in the pattern of ribosome loading on maternal transcripts. In addition to decreased translation, DAZL depletion also causes translational activation of a distinct subset of mRNAs both in quiescent and maturing oocytes, a function recapitulated with YFP-3′UTR reporters. DAZL binds to mRNAs whose translation is both repressed and activated during maturation. Injection of recombinant DAZL protein in DAZL-depleted oocytes rescues the translation and maturation to MII. Mutagenesis of putative DAZL-binding sites in these mRNAs mimics the effect of DAZL depletion. These findings demonstrate that DAZL regulates translation of maternal mRNAs, functioning both as the translational repressor and activator during oocyte maturation. The RNA binding protein DAZL plays a critical role during germ cell development. Here the authors provide evidence that DAZL functions both as activator and repressor of translation during oocyte maturation in mouse.
Refinement Type Contracts for Verification of Scientific Investigative Software

Our scientific knowledge is increasingly built on software output. User code which defines data analysis pipelines and computational models is essential for research in the natural and social sciences, but little is known about how to ensure its correctness. The structure of this code and the development process used to build it limit the utility of traditional testing methodology. Formal methods for software verification have seen great success in ensuring code correctness but generally require more specialized training, development time, and funding than is available in the natural and social sciences. Here, we present a Python library which uses lightweight formal methods to provide correctness guarantees without the need for specialized knowledge or substantial time investment. Our package provides runtime verification of function entry and exit condition contracts using refinement types. It allows checking hyperproperties within contracts and offers automated test case generation to supplement online checking. We co-developed our tool with a medium-sized (\(\approx \)3000 LOC) software package which simulates decision-making in cognitive neuroscience. In addition to helping us locate trivial bugs earlier on in the development cycle, our tool was able to locate four bugs which may have been difficult to find using traditional testing methods. It was also able to find bugs in user code which did not contain contracts or refinement type annotations. This demonstrates how formal methods can be used to verify the correctness of scientific software which is difficult to test with mainstream approaches.
Symmetries and Isomorphisms for Privacy in Control Over the Cloud

Cloud computing platforms are being increasingly used for closing feedback control loops, especially when computationally expensive algorithms, such as model-predictive control, are used to optimize performance. Outsourcing of control algorithms entails an exchange of data between the control system and the cloud and, naturally, raises concerns about the privacy of the control system's data (e.g., state trajectory and control objective). Moreover, any attempt at enforcing privacy needs to add minimal computational overhead to avoid degrading control performance. In this article, we propose several transformation-based methods for enforcing data privacy. We also quantify the amount of provided privacy and discuss how much privacy is lost when the adversary has access to side knowledge. We address three different scenarios: 1) the cloud has no knowledge about the system being controlled; 2) the cloud knows what sensors and actuators the system employs but not the system dynamics; and 3) the cloud knows the system dynamics, its sensors, and actuators. In all of these three scenarios, the proposed methods allow for the control over the cloud without compromising private information (which information is considered private depends on the considered scenario).
Determinants of Global Value Chain Participation : Cross-Country Evidence

The past decades witnessed big changes in international trade with the rise of global value chains. Some countries, such as China, Poland, and Vietnam, rode the tide, while other countries, many in the Africa region, faltered. This paper studies the determinants of participation in global value chains, based on empirical evidence from a panel data set covering more than 100 countries over the past three decades. The evidence shows that factor endowments, geography, political stability, liberal trade policies, foreign direct investment inflows, and domestic industrial capacity are very important in determining participation in global value chains. These factors affect participation in global value chains more than traditional exports.
FQL: An Extensible Feature Query Language and Toolkit on Searching Software Characteristics for HPC Applications.

The amount of large-scale scientific computing software is dramatically increasing. In this work, we designed a new query language, named Feature Query Language (FQL), to collect and extract HPC-related software features or metadata from a quick static code analysis. We also designed and implemented an FQL-based toolkit to automatically detect and present software features using an extensible query repository. A number of large-scale, high performance computing (HPC) scientific applications have been studied in the paper with the FQL toolkit to demonstrate the HPC-related feature extraction and information/metadata collection. Different from the existing static software analysis and refactoring tools which focus on software debug, development and code transformation, the FQL toolkit is simpler, significantly lightweight and strives to collect various and diverse software metadata with ease and rapidly.
A Generalized Proportionate-Type Normalized Subband Adaptive Filter

We show that a new design criterion, i.e., the least squares on subband errors regularized by a weighted norm, can be used to generalize the proportionate-type normalized subband adaptive filtering (PtNSAF) framework. The new criterion directly penalizes subband errors and includes a sparsity penalty term which is minimized using the damped regularized Newton’s method. The impact of the proposed generalized PtNSAF (GPtNSAF) is studied for the system identification problem via computer simulations. Specifically, we study the effects of using different numbers of subbands and various sparsity penalty terms for quasi-sparse, sparse, and dispersive systems. The results show that the benefit of increasing the number of subbands is larger than promoting sparsity of the estimated filter coefficients when the target system is quasi-sparse or dispersive. On the other hand, for sparse target systems, promoting sparsity becomes more important. More importantly, the two aspects provide complementary and additive benefits to the GPtNSAF for speeding up convergence.
The importance of expertise in group decisions

Prior to a collective binary choice, members of a group receive binary signals correlated with the better option. A larger group size may produce less accurate decisions, but expertise is everywhere beneficial. If a group accounts for correlation in signals, a relatively expert member puts an upper bound on the probability of a false belief. The bound holds for any group size and signal distribution. Furthermore, a population investing in expertise is better off cultivating a small mass of elites than adopting an egalitarian policy of education.
Hydrodynamic modeling of mass loss from cataclysmic variable secondaries

Results of detailed computer simulations of mass loss from a cataclysmic variable secondary are presented. The calculations involve solution of the nonlinear hydrodynamical equations of stellar structure under varying degrees of approximation in an attempt to determine stability of the mass loss process. For comparison with previous theoretical studies dynamical sequences were computed assuming spherically symmetric mass loss from the secondary. The assumption of spherical symmetry is very poor since nearly all of the transferred material is lost within a small region about the inner Lagrangian point. Dynamical sequences treating only the region near the Lagrangian point were constructed in a manner consistent with the assumption of Roche geometry. Finally the effects of mass flow nonorthogonal to the Roche equipotential surfaces were treated in a very simple way. The last generalization produces stable mass loss in a model which was unstable for the less realistic approximation schemes. The finding of stable mass transfer implies that instability of the secondary star is not the mechanism leading to cataclysmic variable outbursts. This conclusion is consistent with published observations of dwarf novae made just prior to outburst.
Computer-Based Test Designs

Among the decisions to be made in implementing a computer-based test, the choice of test design is one of the most important. A test design is the manner by which individual items are selected for presentation to examinees during administration. The importance of evaluating test design options is critical because it not only concerns test administration but also basic activities in the test development process and the quality and precision of scores to be obtained for a specified testing purpose. Essentially, conceptualizing the test design options for computerized testing first hinges on the property of being adaptive or not, and then there are varied approaches within each of those two groupings. The purpose of this entry is to provide an overview of selected test designs, adaptive and otherwise, while highlighting certain measurement advantages and concerns associated with each. Keywords: computerized-adaptive testing; computer-based testing; computerized fixed tests; multistage testing; test designs
Is there a timing synergy during multi-finger production of quick force pulses?

We studied whether characteristics of individual finger force profiles covaried across repetitions of a quick force pulse production task to stabilize the required magnitude and timing of the peak force. Subjects produced series of quick force pulses by pressing with all four fingers of the right hand on force sensors under the instruction to keep the magnitude of the peak of total force at 15 N and reach the force peaks at prescribed times. Individual finger force pulses were then reshuffled across trials to create a surrogate data set. The surrogate data set showed a lower average peak force with a larger dispersion. This finding has been interpreted as pointing at predominantly negative covariation among finger force pulses in the actual data that stabilized the required magnitude of the total force, a force synergy. The difference between the actual and surrogate data sets was significant early into the pulse time, starting about 40 ms after the pulse initiation. This finding points at a central nature of the negative covariation without a major role played by visual or proprioceptive feedback. In contrast, the surrogate data set showed smaller dispersion of the timing of the total peak force, suggesting positive covariation of the timings of individual finger force pulses in the actual data interpreted as the lack of a timing synergy. These results have been confirmed with principal component (PC) analysis. The first PC for the timing of the individual finger peak forces accounted for over 90% of the total variance for the actual data set and for under 40% of the total variance for the surrogate data set. The fourth PC for the magnitudes of the finger forces accounted for under 4% of the total variance for the actual data set and for over 15% of the variance for the surrogate data set. The data are interpreted within the uncontrolled manifold hypothesis; they support the hierarchical control scheme suggested by Schoner.
NONLOCAL AUTOMATED SENSITIVITY ANALYSIS

Previously a complete ordinary differential equation (ODE) system was developed for tracking the solution x(~) of a parameterized system of nonlinear equations 0 = ~'(x,~) over an ~-interval (~0, ~). This paper develops a two-phase complex homotopy continuation method for obtaining the required initial conditions at ~t °. An initial "short" artificial continuation is followed by a continuation which essentially proceeds through the physically meaningful function ~, which can ameliorate the problem of artificially induced singularities. Also, the path in the complex plane followed by the continuation parameter in each phase evolves sequentially in an attempt to keep the path both short (minimal number of integration steps) and numerically stable (avoidance of singular points). A FORTRAN program Nasa has been developed for solving the complete ODE system, starting with a two-phase initialization. The program incorporates a fast and efficient procedure for the automatic evaluation of partial derivatives. Numerical experiments are reported which illustrate the program's effectiveness. In Ref. (1) an analytically complete system of ordinary differential equations (ODEs) was developed for finding a solution vector x(~) for a parameterized system of nonlinear equations 0 = ~P(x, ~). The well-known ODE dx(~)/d~ = -(~x)-~ ~ was supplemented with ODEs for the adjoint A (~) and the determinant 6(~) of the Jacobian matrix ~Vx(x(~), ~). This differential system, in principle, permits nonlocal sensitivity analysis, i,e. the tracking of the solution vector x(~) and the sensitivity vector dx(~)/d~, together with the adjoint A(~) and the determinant /i(~), over any closed ~-interval (~0, ~!) where the determinant/i(~) remains nonzero. A FORTRAN program was used successfully in Ref. (1) to solve this differential system for several illustrative examples. Subsequently, the program was modified to incorporate a fast and efficient algorithm Feed for the automatic evaluation of higher-order partial derivatives (2). Nevertheless, to make the program a truly practical tool, a simple and reliable procedure was still needed for obtaining the initial conditions, x(~°), A(~ °) and c~(~°), required by the differential system at the initial parameter point ct °. This paper develops a simple but effective homotopy continuation method for obtaining these initial conditions which differs in two principal respects from standard homotopy continuation methods.~: First, the proposed continuation essentially proceeds through the function ~ rather than through an artificial construct. Letting F(X)D~(X, ~t°), a standard continuation method for finding a solu- tion vector x ° = x(~ °) to the system of equations 0 = F(x) would generally involve solving a system of equations of the form
Chapter 7 – Dry-Steam Power Plants

Dry-steam plants were the first type of geothermal power plants to achieve commercial status. Their history goes back 100 years to 1904 when Prince Piero Ginori Conti built and operated a tiny steam engine using the natural steam jets that issued from the ground at Larderello in the Tuscany region of Italy. Since the geofluid consisted solely of steam, it was fairly easy to hook up a mechanical device to take advantage of the available energy. Although the Prince’s engine only generated enough electrical power to illuminate five light bulbs in his factory, it was the springboard for larger plants.
Evidence of a Modest Price Decline in US Broadband Services

Abstract In this paper, we construct a consumer price index for broadband services in the United States using over 1500 service contracts offered by DSL and cable providers from 2004 through 2009. This exercise frames a range of open questions about measuring price changes in a manner that informs policy discussions about US broadband services. We employ approaches used commonly for constructing a consumer price index by using a mix of matched-model methods and hedonic price index estimations to adjust for qualitative improvements. We find a quality-adjusted price decline, but the evidence points towards a modest decline at most. Our estimates of the price decline range from 3% to 10% in quality-adjusted terms for the 5-years period, which is faster than the BLS estimates for the last 3 years. In contrast to other innovative industries that experience rapid price declines, such as computers or integrated circuits, the modest price decline for broadband services raises many questions.
Concerns about School-Linked Services: Institution-Based versus Community-Based Models.

The systems that serve families and children should address the basic developmental needs of children. Those needs can best be met within a broadly defined service system that offers both services to promote general development as well as services to respond to the specific problems of individual children in trouble. The question the authors address is whether the model of school-linked, integrated services that places the school in the central position to facilitate access to the range of necessary services is the best approach. Although the school may seem like the logical choice as the lead institution, the authors cite arguments against building a governance structure that favors any single institution. They contend that multiple access points are essential for serving all children in a community and that citizens should participate in defining their community's needs and the strategies for meeting them. Chaskin and Richman present an alternative to the school-based model: they describe the community-based model, in which a diversity of service providers, administrative contexts, and institutions work under collaborative governance in a system of linked services. A community-based system involves the major public and private entities in the community, including schools, social services, churches, health providers, and other community organizations which collaborate within a consortium of existing agencies or a newly created entity. (Abstract Adapted from Source: The Future of Children, 1992. Copyright © 1992 by The David and Lucile Packard Foundation) Model School Based Community Based Child Development Youth Development Social Services Intervention 02-04
Vertical ascent from earth to geosynchronous orbit

The concept of ascending vertically from the equator on earth to the point in geosynchronous orbit directly above was investigated. The gravity losses were found to be so great that vertical ascent is not practical with only chemical-rocket propulsion. With laser propulsion, propellant requirements with vertical ascent are reduced and might allow the use of single-stage vehicles from earth to geosynchronous orbit. Combined or composite chemical and laser propulsion is shown to be useful. A gravity ladder suspended from geosynchronous orbit part of the distance to earth is shown to reduce the vehicle propulsion requirements.
Chapter 15 – Mutnovsky Flash-Steam Power Plant, Kamchatka Peninsula, Russia

Publisher Summary The Russian city of Petropavlovsk-Kamchatksy on the Kamchakta Peninsula is 7840 km (4870 mi) and nine time zones east of Moscow. The whole length of the peninsula, about the size of the state of California, is studded with gigantic volcanoes, part of the Pacific Ring of Fire. Kamchatka is home to one of the world's premier geyser fields along the Geysernaya River in the Uzon caldera, so remote that it was not discovered until 1941. Despite its isolated location, Kamchatka was recognized as having great geothermal potential. Renewed interest has resulted in scores of wells being drilled, in numerous geoscientific studies, and technical articles being published and presented to the geothermal community. Vereina using the TOUGH2 reservoir simulator has carried out a detailed study of the reservoir at Mutnovsky. This chapter is based on the conclusions reached in that work. There are two units either under construction or in advanced planning at Mutnovsky: Verkhne-Mutnovsky IV and Mutnovsky second stage. With many advantages for the integrated steam-binary plant, it is likely that future developments at the geothermal fields of Kamchatka will be accomplished with this type of energy conversion system.
Quaternion-Valued Breather Soliton, Rational, and Periodic KdV Solutions

Quaternion-valued solutions to the non-commutative KdV equation are produced using determinants. The solutions produced in this way are (breather) soliton solutions, rational solutions, spatially p...
Persistent media bias

Abstract The news media plays an essential role in society, but surveys indicate that the public views the media as biased. This paper presents a theory of media bias that originates with private information obtained by journalists through their investigations and persists despite profit-maximizing news organizations and rivalry from other news organizations. Bias has two effects on the demand for news. First, rational individuals are more skeptical of potentially biased news and thus rely less on it in their decision-making. This skepticism reduces demand and leads the news organization to set a lower price for its publication the greater is the bias it tolerates. Lower quality news thus commands a lower price. Second, bias makes certain stories more likely than others. Given their private information, journalists may bias their stories if their career prospects can be advanced by being published on the front page. News organizations can control bias by restricting the discretion allowed to journalists, but granting discretion and tolerating bias can increase profits if it allows journalists to be hired at a lower wage. Bias is not driven from the market by a rival news organization nor by a news organization with an opposing bias, and the profits of a high-bias news organization can be higher than the profits of a low bias one. Moreover, bias can be greater with competition than with a monopoly news organization. If individuals collectively choose regulation in place of their individual decision-making, bias increases the expected stringency of regulation.
Inversion of convex ordering in the VIX market

We investigate conditions for the existence of a continuous model on the S&P 500 index (SPX) that jointly calibrates to a full surface of SPX implied volatilities and to the VIX smiles. We present ...
Combining Multiple Functional Connectivity Methods to Improve Causal Inferences

Cognition and behavior emerge from brain network interactions, suggesting that causal interactions should be central to the study of brain function. Yet, approaches that characterize relationships ...
Quantifiable & Comparable Evaluations of Cyber Defensive Capabilities: A Survey & Novel, Unified Approach

Abstract Metrics and frameworks to quantifiably assess security measures have arisen from needs of three distinct research communities—statistical measures from the intrusion detection and prevention literature, evaluation of cyber exercises, e.g., red-team and capture-the-flag competitions, and economic analyses addressing cost-versus-security tradeoffs. In this paper we provide two primary contributions to the security evaluation literature—a representative survey, and a novel framework for evaluating security that is flexible, applicable to all three use cases, and readily interpretable. In our survey of the literature we identify the distinct themes from each community’s evaluation procedures side by side and flesh out the drawbacks and benefits of each. The evaluation framework we propose includes comprehensively modeling the resource, labor, and attack costs in dollars incurred based on expected resource usage, accuracy metrics, and time. This framework provides a unified approach in that it incorporates the accuracy and performance metrics, which dominate intrusion detection evaluation, the time to detection and impact to data and resources of an attack, favored by educational competitions’ metrics, and the monetary cost of many essential security components used in financial analysis. Moreover, it is flexible enough to accommodate each use case, easily interpretable and comparable, and comprehensive in terms of costs considered. Finally, we provide two examples of the framework applied to real-world use cases. Overall, we provide a survey and a grounded, flexible framework with multiple concrete examples for evaluating security which can address the needs of three currently distinct communities.
Non-Asymptotic Analysis of Monte Carlo Tree Search

In this work, we consider the popular tree-based search strategy within the framework of reinforcement learning, the Monte Carlo Tree Search (MCTS), in the context of infinite-horizon discounted cost Markov Decision Process (MDP) with deterministic transitions. While MCTS is believed to provide an approximate value function for a given state with enough simulations, cf. [Kocsis and Szepesvari 2006; Kocsis et al. 2006], the claimed proof of this property is incomplete. This is due to the fact that the variant of MCTS, the Upper Confidence Bound for Trees (UCT), analyzed in prior works utilizes "logarithmic" bonus term for balancing exploration and exploitation within the tree-based search, following the insights from stochastic multi-arm bandit (MAB) literature, cf. [Agrawal 1995; Auer et al. 2002]. In effect, such an approach assumes that the regret of the underlying recursively dependent non-stationary MABs concentrates around their mean exponentially in the number of steps, which is unlikely to hold as pointed out in [Audibert et al. 2009], even for stationary MABs.As the key contribution of this work, we establish polynomial concentration property of regret for a class of non-stationary multi-arm bandits. This in turn establishes that the MCTS with appropriate polynomial rather than logarithmic bonus term in UCB has the claimed property of [Kocsis and Szepesvari 2006; Kocsis et al. 2006]. Interestingly enough, empirically successful approaches (cf. [Silver et al. 2017]) utilize a similar polynomial form of MCTS as suggested by our result. Using this as a building block, we argue that MCTS, combined with nearest neighbor supervised learning, acts as a "policy improvement" operator, i.e., it iteratively improves value function approximation for all states, due to combining with supervised learning, despite evaluating at only finitely many states. In effect, we establish that to learn an e-approximation of the value function for deterministic MDPs with respect to l∞ norm, MCTS combined with nearest neighbor requires a sample size scaling as O (e-(d+4), where d is the dimension of the state space. This is nearly optimal due to a minimax lower bound of ∼Ω (e-(d+2) [Shah and Xie 2018], suggesting the strength of the variant of MCTS we propose here and our resulting analysis.
Distinct Components of Photoperiodic Light Are Differentially Encoded by the Mammalian Circadian Clock.

Seasonal light cycles influence multiple physiological functions and are mediated through photoperiodic encoding by the circadian system. Despite our knowledge of the strong connection between seas...
QuASE: Question-Answer Driven Sentence Encoding.

Question-answering (QA) data often encodes essential information in many facets. This paper studies a natural question: Can we get supervision from QA data for other tasks (typically, non-QA ones)? For example, can we use QAMR (Michael et al., 2017) to improve named entity recognition? We suggest that simply further pre-training BERT is often not the best option, and propose the question-answer driven sentence encoding (QuASE) framework. QuASE learns representations from QA data, using BERT or other state-of-the-art contextual language models. In particular, we observe the need to distinguish between two types of sentence encodings, depending on whether the target task is a single- or multi-sentence input; in both cases, the resulting encoding is shown to be an easy-to-use plugin for many downstream tasks. This work may point out an alternative way to supervise NLP tasks.
Identification and genomic analysis of pedigrees with exceptional longevity identifies candidate rare variants.

Abstract Background Longevity as a phenotype entails living longer than average and typically includes living without chronic age-related diseases. Recently, several common genetic components to longevity have been identified. This study aims to identify additional genetic variants associated with longevity using unique and powerful analyses of pedigrees with a statistical excess of healthy elderly individuals identified in the Utah Population Database (UPDB). Methods From an existing biorepository of Utah pedigrees, six independent cousin pairs were selected from four extended pedigrees that exhibited an excess of healthy elderly individuals; whole exome sequencing (WES) was performed on two elderly individuals from each pedigree who were either first cousins or first cousins once removed. Rare ( Results Fifteen rare candidate genetic variants spanning 17 genes shared within cousins were identified as having passed prioritization criteria. Of those variants, six were present in genes that are known or predicted to affect the aging process: rs78408340 (PAM), rs112892337 (ZFAT), rs61737629 (ESPL1), rs141903485 (CEBPE), rs144369314 (UTP4), and rs61753103 (NUP88 and RABEP1). ESPL1 rs61737629 and CEBPE rs141903485 show additional evidence of segregation with longevity in expanded pedigree analyses (p-values = .001 and .0001, respectively). Discussion This unique pedigree analysis efficiently identified several novel rare candidate variants that may affect the aging process and added support to seven genes that likely contribute to longevity. Further analyses showed evidence for segregation for two rare variants, ESPL1 rs61737629 and CEBPE rs141903485, in the original longevity pedigrees in which they were initially observed. These candidate genes and variants warrant further investigation.
Interpolation for Brill-Noether curves in $\mathbb{P}^4$

We compute the number of general points through which a general Brill–Noether curve in $${\mathbb {P}}^4$$ passes. We also prove an analogous theorem when some points are constrained to lie in a transverse hyperplane. As explained in [10], these results play an essential role in the first author’s proof of the Maximal Rank Conjecture [9].
HAPPI GWAS: Holistic Analysis with Pre- and Post-Integration GWAS.

Motivation Advanced publicly available sequencing data from large populations have enabled informative genome-wide association studies (GWAS) that associate SNPs with phenotypic traits of interest. Many publicly available tools able to perform GWAS have been developed in response to increased demand. However, these tools lack a comprehensive pipeline that includes both pre-GWAS analysis, such as outlier removal, data transformation and calculation of Best Linear Unbiased Predictions or Best Linear Unbiased Estimates. In addition, post-GWAS analysis, such as haploblock analysis and candidate gene identification, is lacking. Results Here, we present Holistic Analysis with Pre- and Post-Integration (HAPPI) GWAS, an open-source GWAS tool able to perform pre-GWAS, GWAS and post-GWAS analysis in an automated pipeline using the command-line interface. Availability and implementation HAPPI GWAS is written in R for any Unix-like operating systems and is available on GitHub (https://github.com/Angelovici-Lab/HAPPI.GWAS.git). Supplementary information Supplementary data are available at Bioinformatics online.
Duty to Warn in Strategic Games

The paper investigates the second-order blameworthiness or duty to warn modality "one coalition knew how another coalition could have prevented an outcome''. The main technical result is a sound and complete logical system that describes the interplay between the distributed knowledge and the duty to warn modalities.
Shape curvature effects in viscous streaming

Viscous streaming flows generated by objects of constant curvature (circular cylinders, infinite plates) have been well understood. Yet, characterization and understanding of such flows when multiple body length scales are involved has not been looked into in rigorous detail. We propose a simplified setting to understand and explore the effect of multiple body curvatures on streaming flows, analysing the system through the lens of bifurcation theory. Our set-up consists of periodic, regular lattices of cylinders characterized by two distinct radii, so as to inject discrete curvatures into the system, which in turn affect the streaming field generated due to an oscillatory background flow. We demonstrate that our understanding based on this system, and in particular the role of bifurcations in determining the local flow topology, can be then generalized to a variety of individual convex shapes presenting a spectrum of curvatures, explaining prior experimental and computational observations. Thus, this study illustrates a route towards the rational manipulation of viscous streaming flow topology, through regulated variation of object geometry.
An Overview of Utilizing Knowledge Bases in Neural Networks for Question Answering

Question Answering (QA) requires understanding of queries expressed in natural languages and identification of relevant information content to provide an answer. For closed-world QAs, information access is obtained by means of either context texts, or a Knowledge Base (KB), or both. KBs are human-generated schematic representations of world knowledge. The representational ability of neural networks to generalize world information makes it an important component of current QA research. In this paper, we study the neural networks and QA systems in the context of KBs. Specifically, we focus on surveying methods for KB embedding, how such embeddings are integrated into the neural networks, and the role such embeddings play in improving performance across different question-answering problems. Our study of multiple question answering methods finds that the neural networks are able to produce state-of-art results in different question answering domains, and inclusion of additional information via KB embeddings further improve the performance of such approaches. Further progress in QA can be improved by incorporating more powerful representations of KBs.
Fitting a Kalman Smoother to Data.

This paper considers the problem of fitting the parameters in a Kalman smoother to data. We formulate the Kalman smoothing problem with missing measurements as a constrained least squares problem and provide an efficient solution method based on sparse linear algebra. We then introduce the Kalman smoother tuning problem, which seeks to adjust parameters in the Kalman smoother to achieve low prediction error on held out measurements. We derive a Kalman smoother auto-tuning algorithm, which is based on the proximal gradient method, that finds good, if not the best, parameters for a given dataset. Central to our method is the computation of the gradient of the prediction error on the held out measurements with respect to the parameters of the Kalman smoother; we describe how to compute the gradient at little to no additional cost. We demonstrate the method on population migration within the United States as well as data collected from a smartphone's IMU+GPS system while driving.
RNAAgeCalc: A multi-tissue transcriptional age calculator

Biological aging reflects decline in physiological functions and is an effective indicator of morbidity and mortality. Numerous epigenetic age calculators are available, however biological aging calculators based on transcription remain scarce. Here, we introduce RNAAgeCalc, a versatile across-tissue and tissue-specific transcriptional age calculator. By performing a meta-analysis of transcriptional age signature across multi-tissues using the GTEx database, we identify 1,616 common age-related genes, as well as tissue-specific age-related genes. Based on these genes, we develop new across-tissue and tissue-specific age predictors. We show that our transcriptional age calculator outperforms other prior age related gene signatures as indicated by the higher correlation with chronological age as well as lower median and median error. Our results also indicate that both racial and tissue differences are associated with transcriptional age. Furthermore, we demonstrate that the transcriptional age acceleration computed from our within-tissue predictor is significantly correlated with mutation burden, mortality risk and cancer stage in several types of cancer from the TCGA database, and offers complementary information to DNA methylation age. RNAAgeCalc is available at http://www.ams.sunysb.edu/~pfkuan/softwares.html#RNAAgeCalc, both as Bioconductor and Python packages, accompanied by a user-friendly interactive Shiny app.
Design of compositionally graded contact layers for MOCVD grown high Al-content AlGaN transistors

In this letter, we design and demonstrate an improved metalorganic chemical vapor deposition (MOCVD) grown reverse Al-composition graded contact layer, whereby the Al-composition of AlxGa1−xN in the contact layer is graded from the higher Al-composition as in the channel to lower Al-composition, to achieve a low resistance contact to MOCVD grown ultrawide bandgap Al0.70Ga0.30N channel metal-semiconductor field-effect transistors. Increasing the thickness of the reverse graded layer was found to improve contact layer resistance significantly, leading to a contact resistivity of 3.3 × 10−5 Ω cm2. Devices with a gate length, LG, of 0.6 μm and a source-drain spacing, LSD, of 1.5 μm displayed a maximum current density, IDS,MAX, of 635 mA/mm with an applied gate voltage, VGS, of +2 V. Breakdown measurements on transistors with a gate to drain spacing, LGD, of 770 nm had breakdown voltage greater than 220 V, corresponding to a minimum breakdown field of 2.86 MV/cm—almost 3× higher than that exhibited by lateral GaN channel devices with similar dimensions. This work provides a framework for the design of low resistance contacts to MOCVD grown high Al-content AlxGa1−xN channel transistors.
Passive Appreciation in Divorce: A Quantitative Measure

Breaking up is hard to do. High net worth marital estates often contain family businesses started or inherited by one or both spouses. The growth in the value of such business interests occurring during the marriage can consist of two components. It may be attributable to environmental factors (passive) or marital efforts and resources (active). Quantifying the passive contribution of economic environment changes during the marriage is a complex task. A substantial body of case law dealing with establishing causation and attributing impact has developed in the torts and class action practice areas. This paper presents this statistically sound, empirically tested, and peer reviewed methodology for estimating the passive (caused by/resulting from external forces) portion of appreciation for a business. This methodology can assist the forensic accountants in identifying pertinent causal factors and quantifying their impact (passive appreciation) on the value of a business during a marriage.