cssi/SciSciGPT-SciSciNet huggingface dataset:
On variational solutions for whole brain serial-section histology using a Sobolev prior in the computational anatomy random orbit model

This paper presents a variational framework for dense diffeomorphic atlas-mapping onto high-throughput histology stacks at the 20 μm meso-scale. The observed sections are modelled as Gaussian random fields conditioned on a sequence of unknown section by section rigid motions and unknown diffeomorphic transformation of a three-dimensional atlas. To regularize over the high-dimensionality of our parameter space (which is a product space of the rigid motion dimensions and the diffeomorphism dimensions), the histology stacks are modelled as arising from a first order Sobolev space smoothness prior. We show that the joint maximum a-posteriori, penalized-likelihood estimator of our high dimensional parameter space emerges as a joint optimization interleaving rigid motion estimation for histology restacking and large deformation diffeomorphic metric mapping to atlas coordinates. We show that joint optimization in this parameter space solves the classical curvature non-identifiability of the histology stacking problem. The algorithms are demonstrated on a collection of whole-brain histological image stacks from the Mouse Brain Architecture Project.
Identifying group contributions in NBA lineups with spectral analysis

We address the question of how to quantify the contributions of groups of players to team success. Our approach is based on spectral analysis, a technique from algebraic signal processing, which has several appealing features. First, our analysis decomposes the team success signal into components that are naturally understood as the contributions of player groups of a given size: individuals, pairs, triples, fours, and full five-player lineups. Secondly, the decomposition is orthogonal so that contributions of a player group can be thought of as pure: Contributions attributed to a group of three, for example, have been separated from the lower-order contributions of constituent pairs and individuals. We present detailed a spectral analysis using NBA play-by-play data and show how this can be a practical tool in understanding lineup composition and utilization.
Predicting mechanism of action of cellular perturbations with pathway activity signatures.

Motivation Misregulation of signaling pathway activity is etiologic for many human diseases, and modulating activity of signaling pathways is often the preferred therapeutic strategy. Understanding the mechanism of action (MOA) of bioactive chemicals in terms of targeted signaling pathways is the essential first step in evaluating their therapeutic potential. Changes in signaling pathway activity are often not reflected in changes in expression of pathway genes which makes MOA inferences from transcriptional signatures (TSeses) a difficult problem. Results We developed a new computational method for implicating pathway targets of bioactive chemicals and other cellular perturbations by integrated analysis of pathway network topology, the Library of Integrated Network-based Cellular Signature TSes of genetic perturbations of pathway genes and the TS of the perturbation. Our methodology accurately predicts signaling pathways targeted by the perturbation when current pathway analysis approaches utilizing only the TS of the perturbation fail. Availability and implementation Open source R package paslincs is available at https://github.com/uc-bd2k/paslincs. Supplementary information Supplementary data are available at Bioinformatics online.
A high-order numerical approach with Cartesian meshes for modeling of wave propagation and heat transfer on irregular domains with inhomogeneous materials

Abstract Recently we have developed a new numerical approach for PDEs with constant coefficients on irregular domains and Cartesian meshes. In this paper we extend it to a much more general case of PDEs with variable coefficients that have a lot of applications; e.g., the modeling of functionally graded materials, the inhomogeneous materials obtained by 3-D printing and many others. Here, we consider the 2-D wave and heat equations for isotropic and anisotropic inhomogeneous materials. The idea of the extension to the case of PDEs with variable coefficients is based on the representation of the stencil coefficients as functions of the mesh size. This leads to the increase in the size of the local system of algebraic equations solved for each grid point of the new approach; however, this does not change the size of the global system of semidiscrete equations and practically does not increase the computational costs of the proposed technique. Similar to our previous technique, the new 2-D approach with compact 9-point stencils uses trivial Cartesian meshes for complex irregular domains and provides the fourth order of accuracy for the wave and heat equations with variable coefficients. The calculation of the coefficients of the stencil equations is based on the minimization of the local truncation error of the stencil equations and yields the optimal order of accuracy of the new technique. At similar 9-point stencils, the accuracy of the new approach is much higher than that for the linear finite elements. The numerical results for irregular domains show that at the same number of degrees of freedom, the new approach is even much more accurate than the high-order (up to the third order) finite elements with much wider stencils. The wave and heat equations are uniformly treated with the new approach.
Phenotypic and physiological responses to salt exposure in Sorghum reveal diversity among domesticated landraces

Premise Soil salinity negatively impacts plant function, development, and yield. To overcome this impediment to agricultural productivity, variation in morphological and physiological response to salinity among genotypes of important crops should be explored. Sorghum bicolor is a staple crop that has adapted to a variety of environmental conditions and contains a significant amount of standing genetic diversity, making it an exemplary species to study variation in salinity tolerance. Methods Twenty-one diverse Sorghum accessions were treated with nonsaline water or 75 mM sodium chloride. Salinity tolerance was assessed via changes in biomass between control and salt-treated individuals. Accessions were first rank-ordered for salinity tolerance, and then individuals spanning a wide range of responses were analyzed for foliar proline and ion accumulation. Tolerance rankings were then overlaid on a neighbor-joining tree. Results We found that, while proline is often a good indicator of osmotic adjustment and is historically associated with increased salt tolerance in many species, proline accumulation in sorghum reflects a stress response injury rather than acclimation. When combining ion profiles with stress tolerance indices, the variation observed in tolerance was not a sole result of Na+ accumulation, but rather reflected accession-specific mechanisms. Conclusions We identified significant variation in salinity tolerance among Sorghum accessions that may be a result of the domestication history of Sorghum. When we compared our results with known phylogenetic relationships within sorghum, the most parsimonious explanation for our findings is that salinity tolerance was acquired early during domestication and subsequently lost in accessions growing in areas varying in soil salinity.
On the complexity of modulo-q arguments and the chevalley-warning theorem

We study the search problem class PPAq defined as a modulo-q analog of the well-known polynomial parity argument class PPA introduced by Papadimitriou (JCSS 1994). Our first result shows that this class can be characterized in terms of PPAp for prime p.Our main result is to establish that an explicit version of a search problem associated to the Chevalley-Warning theorem is complete for PPAp for prime p. This problem is natural in that it does not explicitly involve circuits as part of the input. It is the first such complete problem for PPAp when p ≥ 3.Finally we discuss connections between Chevalley-Warning theorem and the well-studied short integer solution problem and survey the structural properties of PPAq.
A demographic approach to understanding the effects of climate on population growth

Amphibian life history traits are affected by temperature and precipitation. Yet, connecting these relationships to population growth, especially for multiple populations within a species, is lacking and precludes our understanding of amphibian population dynamics and distributions. Therefore, we constructed integral projection models for five populations along an elevational gradient to determine how climate and season affect population growth of a terrestrial salamander Plethodon montanus and the importance of demographic vital rates to population growth under varying climate scenarios. We found that population growth was typically higher at the highest elevation compared to the lower elevations, whereas varying inactive season conditions, represented by the late fall, winter and early spring, produced a greater variation in population growth than varying active season conditions (late spring, summer, and early fall). Furthermore, survival and growth were consistently more important, as measured by elasticity, compared to fecundity, and large females had the greatest elasticity compared to all other body sizes. Our results suggest that changing inactive season conditions, especially those that would affect the survival of large individuals, may have the greatest impact on population growth. We recommend future experimental studies focus on the inactive season to better elucidate the mechanisms by which these conditions can affect survival.
One gene, multiple ecological strategies: A biofilm regulator is a capacitor for sustainable diversity.

Many bacteria cycle between sessile and motile forms in which they must sense and respond to internal and external signals to coordinate appropriate physiology. Maintaining fitness requires genetic networks that have been honed in variable environments to integrate these signals. The identity of the major regulators and how their control mechanisms evolved remain largely unknown in most organisms. During four different evolution experiments with the opportunist betaproteobacterium Burkholderia cenocepacia in a biofilm model, mutations were most frequently selected in the conserved gene rpfR. RpfR uniquely integrates two major signaling systems—quorum sensing and the motile–sessile switch mediated by cyclic-di-GMP—by two domains that sense, respond to, and control the synthesis of the autoinducer cis-2-dodecenoic acid (BDSF). The BDSF response in turn regulates the activity of diguanylate cyclase and phosphodiesterase domains acting on cyclic-di-GMP. Parallel adaptive substitutions evolved in each of these domains to produce unique life history strategies by regulating cyclic-di-GMP levels, global transcriptional responses, biofilm production, and polysaccharide composition. These phenotypes translated into distinct ecology and biofilm structures that enabled mutants to coexist and produce more biomass than expected from their constituents grown alone. This study shows that when bacterial populations are selected in environments challenging the limits of their plasticity, the evolved mutations not only alter genes at the nexus of signaling networks but also reveal the scope of their regulatory functions.
Estimating DSGE Models: Recent Advances and Future Challenges

We review the current state of the estimation of dynamic stochastic general equilibrium (DSGE) models. After introducing a general framework for dealing with DSGE models, the state-space representa...
Hardness of Sparse Sets and Minimal Circuit Size Problem

We study the magnification of hardness of sparse sets in nondeterministic time complexity classes on a randomized streaming model. One of our results shows that if there exists a \(2^{n^{o(1)}}\)-sparse set in \(\mathrm{NDTIME}(2^{n^{o(1)}})\) that does not have any randomized streaming algorithm with \(n^{o(1)}\) updating time, and \(n^{o(1)}\) space, then \(\mathrm{NEXP}\not =\mathrm{BPP}\), where a f(n)-sparse set is a language that has at most f(n) strings of length n. We also show that if \(\mathrm{MCSP}\) is \(\mathrm{ZPP}\)-hard under polynomial time truth-table reductions, then \(\mathrm{EXP}\not =\mathrm{ZPP}\).
Hidden dynamic signatures drive substrate selectivity in the disordered phosphoproteome.

Phosphorylation sites are hyperabundant in the eukaryotic disordered proteome, suggesting that conformational fluctuations play a major role in determining to what extent a kinase interacts with a particular substrate. In biophysical terms, substrate selectivity may be determined not just by the structural–chemical complementarity between the kinase and its protein substrates but also by the free energy difference between the conformational ensembles that are, or are not, recognized by the kinase. To test this hypothesis, we developed a statistical-thermodynamics-based informatics framework, which allows us to probe for the contribution of equilibrium fluctuations to phosphorylation, as evaluated by the ability to predict Ser/Thr/Tyr phosphorylation sites in the disordered proteome. Essential to this framework is a decomposition of substrate sequence information into two types: vertical information encoding conserved kinase specificity motifs and horizontal information encoding substrate conformational equilibrium that is embedded, but often not apparent, within position-specific conservation patterns. We find not only that conformational fluctuations play a major role but also that they are the dominant contribution to substrate selectivity. In fact, the main substrate classifier distinguishing selectivity is the magnitude of change in local compaction of the disordered chain upon phosphorylation of these mostly singly phosphorylated sites. In addition to providing fundamental insights into the consequences of phosphorylation across the proteome, our approach provides a statistical-thermodynamic strategy for partitioning any sequence-based search into contributions from structural–chemical complementarity and those from changes in conformational equilibrium.
Effect of aspect ratio on cross-flow turbine performance

Cross-flow turbines convert kinetic power in wind or water currents to mechanical power. Unlike axial-flow turbines, the influence of geometric parameters on turbine performance is not well-understood, in part because there are neither generalized analytical formulations nor inexpensive, accurate numerical models that describe their fluid dynamics. Here, we experimentally investigate the effect of aspect ratio—the ratio of the blade span to rotor diameter—on the performance of a straight-bladed cross-flow turbine in a water channel. To isolate the effect of aspect ratio, all other non-dimensional parameters are held constant, including the relative confinement, Froude number, and Reynolds number. The coefficient of performance is found to be invariant for the range of aspect ratios tested (0.95–1.63), which we ascribe to minimal blade–support interactions for this turbine design. Finally, a subset of experiments is repeated without controlling for the Froude number, and the coefficient of performance is found to increase, a consequence of the Froude number variation that could mistakenly be ascribed to aspect ratio. This highlights the importance of a rigorous experimental design when exploring the effect of geometric parameters on cross-flow turbine performance.
Parallelism in Randomized Incremental Algorithms

In this article, we show that many sequential randomized incremental algorithms are in fact parallel. We consider algorithms for several problems, including Delaunay triangulation, linear programming, closest pair, smallest enclosing disk, least-element lists, and strongly connected components. We analyze the dependencies between iterations in an algorithm and show that the dependence structure is shallow with high probability or that, by violating some dependencies, the structure is shallow and the work is not increased significantly. We identify three types of algorithms based on their dependencies and present a framework for analyzing each type. Using the framework gives work-efficient polylogarithmic-depth parallel algorithms for most of the problems that we study. This article shows the first incremental Delaunay triangulation algorithm with optimal work and polylogarithmic depth. This result is important, since most implementations of parallel Delaunay triangulation use the incremental approach. Our results also improve bounds on strongly connected components and least-element lists and significantly simplify parallel algorithms for several problems.
In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

Subsurface microbial communities mediate the transformation and fate of redox sensitive materials including organic matter, metals and radionuclides. Few studies have explored how changing geochemical conditions influence the composition of groundwater microbial communities over time. We temporally monitored alterations in abiotic forces on microbial community structure using 1L in-field bioreactors receiving background and contaminated groundwater at the Oak Ridge Reservation, TN. Planktonic and biofilm microbial communities were initialized with background water for 4 days to establish communities in triplicate control reactors and triplicate test reactors and then fed filtered water for 14 days. On day 18, three reactors were switched to receive filtered groundwater from a contaminated well, enriched in total dissolved solids relative to the background site, particularly chloride, nitrate, uranium, and sulfate. Biological and geochemical data were collected throughout the experiment, including planktonic and biofilm DNA for 16S rRNA amplicon sequencing, cell counts, total protein, anions, cations, trace metals, organic acids, bicarbonate, pH, Eh, DO, and conductivity. We observed significant shifts in both planktonic and biofilm microbial communities receiving contaminated water. This included a loss of rare taxa, especially amongst members of the Bacteroidetes, Acidobacteria, Chloroflexi, and Betaproteobacteria, but enrichment in the Fe- and nitrate- reducing Ferribacterium and parasitic Bdellovibrio. These shifted communities were more similar to the contaminated well community, suggesting that geochemical forces substantially influence microbial community diversity and structure. These influences can only be captured through such comprehensive temporal studies, which also enable more robust and accurate predictive models to be developed.
Electromagnetic Response of Ballistic Metamaterials

The electromagnetic response of ballistic metamaterials, metal-dielectric composites with the unit cell size smaller than electron mean free path, is defined by the surface scattering of the free electrons at the metal-dielectric interface.
Understand Variability of COVID-19 Through Population and Tissue Variations in Expression of SARS-CoV-2 Host Genes

An urgent question of coronavirus disease 2019 (COVID-19) is population variation in susceptibility to SARS-CoV-2 infection and symptom severity. We explore the expression profiles of SARS-CoV-2 host genes, their population variations, associated genetic variants, age- and sex-dependency in normal individuals. SARS-CoV-2 host genes are provisionally defined as the human genes that are experimentally validated or bioinformatically predicted to interact with SARS-CoV-2 proteins. Genes exhibiting most variable expression include ACE2, CLEC4G, CLEC4M, CD209 (interact with the SARS-CoV-2 spike protein); REEP6 (a receptor accessory protein expressed in the olfactory epithelium); SLC27A2 and PKP2 (inhibit virus replication); and PTGS2 (mediates fever response). SNP rs4804803, associated with SARS severity, affects expression of CLEC4G and CD209. Genetic variants of proteases associated with SARS-CoV-2 entry (TMPRSS2, CTSB, and CTSL) are strongly associated with their expression variation, suggesting a genetic contribution to phenotypic variations in multiple organs upon virus attack. The most significant age-dependent gene is ACE2, the cellular receptor of SARS-CoV-2. Others include TGF-β family member GDF15, mediating inflammation, and VKORC1, possibly explaining vitamin K deficiency in COVID-19. TIMM10 and ERGIC1 exhibit significant sex differences. In summary, our results show genetic and multiple biological variables may underlie the population variation in SARS-CoV-2 infection and symptom severity.
Simultaneous Learning from Human Pose and Object Cues for Real-Time Activity Recognition

Real-time human activity recognition plays an essential role in real-world human-centered robotics applications, such as assisted living and human-robot collaboration. Although previous methods based on skeletal data to encode human poses showed promising results on real-time activity recognition, they lacked the capability to consider the context provided by objects within the scene and in use by the humans, which can provide a further discriminant between human activity categories. In this paper, we propose a novel approach to real-time human activity recognition, through simultaneously learning from observations of both human poses and objects involved in the human activity. We formulate human activity recognition as a joint optimization problem under a unified mathematical framework, which uses a regression-like loss function to integrate human pose and object cues and defines structured sparsity-inducing norms to identify discriminative body joints and object attributes. To evaluate our method, we perform extensive experiments on two benchmark datasets and a physical robot in a home assistance setting. Experimental results have shown that our method outperforms previous methods and obtains real-time performance for human activity recognition with a processing speed of 104 Hz.
The effects of the Summer All Out Foot Patrol Initiative in New York City: a difference-in-differences approach

The New York City Police Department’s “Summer All Out” (SAO) initiative was a 90-day, presence-based foot patrol program in a subset of the city’s patrol jurisdictions. We assessed the effectiveness of SAO initiative in reducing crime and gun violence using a difference-in-differences (DiD) approach. Results indicate the SAO initiative was only associated with significant reductions in specific property offenses, not violent crime rates. Foot patrols did not have a strong, isolating impact on violent street crime in 2014 or 2015. Deployments on foot across expansive geographies also have a weak, negligible influence on open-air shootings. The findings suggest saturating jurisdictions with high-visibility foot patrols has little influence on street-level offending, with no anticipatory or persistent effects. Police departments should exercise caution in deploying foot patrols over large patrol jurisdictions.
A Minimal Biophysical Model of Neocortical Pyramidal Cells: Implications for Frontal Cortex Microcircuitry and Field Potential Generation.

Ca2+ spikes initiated in the distal trunk of layer 5 pyramidal cells (PCs) underlie nonlinear dynamic changes in the gain of cellular response, critical for top-down control of cortical processing. Detailed models with many compartments and dozens of ionic channels can account for this Ca2+ spike-dependent gain and associated critical frequency. However, current models do not account for all known Ca2+-dependent features. Previous attempts to include more features have required increasing complexity, limiting their interpretability and utility for studying large population dynamics. We overcome these limitations in a minimal two-compartment biophysical model. In our model, a basal-dendrites/somatic compartment included fast-inactivating Na+ and delayed-rectifier K+ conductances, while an apical-dendrites/trunk compartment included persistent Na+, hyperpolarization-activated cation (Ih), slow-inactivating K+, muscarinic K+, and Ca2+ L-type. The model replicated the Ca2+ spike morphology and its critical frequency plus three other defining features of layer 5 PC synaptic integration: linear frequency-current relationships, back-propagation-activated Ca2+ spike firing, and a shift in the critical frequency by blocking Ih. Simulating 1000 synchronized layer 5 PCs, we reproduced the current source density patterns evoked by Ca2+ spikes and describe resulting medial-frontal EEG on a male macaque monkey. We reproduced changes in the current source density when Ih was blocked. Thus, a two-compartment model with five crucial ionic currents in the apical dendrites reproduces all features of these neurons. We discuss the utility of this minimal model to study the microcircuitry of agranular areas of the frontal lobe involved in cognitive control and responsible for event-related potentials, such as the error-related negativity. SIGNIFICANCE STATEMENT A minimal model of layer 5 pyramidal cells replicates all known features crucial for distal synaptic integration in these neurons. By redistributing voltage-gated and returning transmembrane currents in the model, we establish a theoretical framework for the investigation of cortical microcircuit contribution to intracranial local field potentials and EEG. This tractable model will enable biophysical evaluation of multiscale electrophysiological signatures and computational investigation of cortical processing.
Dynamics of a qubit-oscillator system with periodically varying coupling

The dynamics of qubits coupled to a harmonic oscillator with time-periodic coupling is investigated in the framework of Floquet theory. This system can be used to model nonadiabatic phenomena that require a periodic modulation of the qubit/oscillator coupling. The case of a single qubit coupled to a resonator populated with $n= 0,1$ photons is explicitly treated. The time-dependent Schrodinger equation describing the system's dynamics is solved within the Floquet formalism and a perturbative approach in the time- and Laplace-domain. Good quantitative agreement is found between the analytical and numerical calculations within the Floquet approach, making it the most promising candidate for the study of time-periodic problems. Nonetheless, the time- or Laplace-domain perturbative approaches can be used in the presence of aperiodic time-dependent terms in the Hamiltonian.
Rsp activates expression of the Cnt system in Staphylococcus aureus.

The Cnt system is crucial for the optimal import of essential metals in metal-limiting conditions and contributes to virulence in S. aureus. In a screen for regulators of efflux pumps in a phage-based ultra-high-density transposon library, we identified Rsp as a candidate regulator of the cntE gene. A two-fold decrease in expression of all genes of the cnt operon was observed by RT-qPCR in the rsp mutant compared to the parental strain, indicating that Rsp acts as an activator of the cnt operon. To determine whether the Rsp activation depends on iron, we compared mutant and parent cnt expression under varying metal conditions. A 2-fold reduction in cnt gene expression was detected in the rsp mutant in TSB, and a slightly smaller decrease (1.9, 1.7, and 1.5-fold changes for cntK, cmtA, and cntE respectively) was observed after addition of dipyridyl. The greatest decrease was seen with addition of FeSO4 (4.1, 5.3 and 6.3-fold changes for cntK, cmtA and cntE respectively). These findings suggest that Rsp activates the cnt operon in low and high iron conditions. To study the relationship between Rsp and the cnt repressors Fur and Zur, we created single and double mutants. Both fur and zur single mutants had significant increases in cnt gene expression compared to the parental strain, as did the fur rsp double mutant. The zur rsp double mutant also had a significant increase in cntK expression and a trend in increases in cntA and cntE expression just below statistical significance. Thus, the ability of Fur and Zur to repress cnt gene expression are not eliminated by the presence of Rsp. However, there were significantly smaller increases in cnt gene expression in the double mutants compared to single mutants, suggesting that Rsp activation can still occur in the absence of these repressors. To determine if Rsp directly modulates expression of cnt genes, incubation of purified Rsp caused a DNA-specific band shift for the cntK and cntA promoters. Rsp activation may act to maintain basal cellular levels of staphylopine to scavenge free metals when needed, in addition to metal dependent regulation by Fur and Zur.
Seemingly stable chemical kinetics can be stable, marginally stable, or unstable

We present three examples of chemical reaction networks whose ordinary differential equation scaling limit are almost identical and in all cases stable. Nevertheless, the Markov jump processes associated to these reaction networks display the full range of behaviors: one is stable (positive recurrent), one is unstable (transient) and one is marginally stable (null recurrent). We study these differences and characterize the invariant measures by Lyapunov function techniques. In particular, we design a natural set of such functions which scale homogeneously to infinity, taking advantage of the same scaling behavior of the reaction rates.
Differential gene expression analysis and cytological evidence reveal a sexual stage of an amoeba with multiparental cellular and nuclear fusion

Sex is a hallmark of eukaryotes but its evolution in microbial eukaryotes is poorly elucidated. Recent genomic studies revealed microbial eukaryotes possess a genetic toolkit necessary for sexual reproduction. However, the mechanism of sexual development in a majority of microbial eukaryotes including amoebozoans is poorly characterized. The major hurdle in studying sex in microbial eukaryotes is a lack of observational evidence, primarily due to its cryptic nature. In this study, we used a tractable fusing amoeba, Cochliopodium, to investigate sexual development using stage-specific Differential Gene Expression (DGE) and cytological analyses. Both DGE and cytological results showed that most of the meiosis and sex-related genes are upregulated in Cochliopodium undergoing fusion in laboratory culture. Relative gene ontology (GO) category representations in unfused and fused cells revealed a functional skew of the fused transcriptome toward DNA metabolism, nucleus and ligases that are suggestive of a commitment to sexual development. However, the GO categories of unfused cells were dominated by metabolic pathways and other processes indicative of a vegetative phase. Our study provides strong evidence that the fused cells represent a sexual stage in Cochliopodium. Our findings have further implications in understanding the evolution and mechanism of inheritance involving multiparents in other eukaryotes with a similar reproductive strategy.
Exploring Whether Super-puffs can be Explained as Ringed Exoplanets

An intriguing, growing class of planets are the "super-puffs," objects with exceptionally large radii for their masses and thus correspondingly low densities (≾0.3 g cm⁻³). Here we consider whether they could have large inferred radii because they are in fact ringed. This would naturally explain why super-puffs have thus far only shown featureless transit spectra. We find that this hypothesis can work in some cases but not all. The close proximity of the super-puffs to their parent stars necessitates rings with a rocky rather than icy composition. This limits the radius of the rings, and makes it challenging to explain the large size of Kepler 51b, 51c, 51d, and 79d unless the rings are composed of porous material. Furthermore, the short tidal locking timescales for Kepler 18d, 223d, and 223e mean that these planets may be spinning too slowly, resulting in a small oblateness and rings that are warped by their parent star. Kepler 87c and 177c have the best chance of being explained by rings. Using transit simulations, we show that testing this hypothesis requires photometry with a precision of somewhere between ~10 ppm and ~50 ppm, which roughly scales with the ratio of the planet and star's radii. We conclude with a note about the recently discovered super-puff HIP 41378f.
Biases in Metallicity Measurements from Global Galaxy Spectra: The Effects of Flux Weighting and Diffuse Ionized Gas Contamination

Galaxy metallicity scaling relations provide a powerful tool for understanding galaxy evolution, but obtaining unbiased global galaxy gas-phase oxygen abundances requires proper treatment of the various line-emitting sources within spectroscopic apertures. We present a model framework that treats galaxies as ensembles of HII and diffuse ionized gas (DIG) regions of varying metallicities. These models are based upon empirical relations between line ratios and electron temperature for HII regions, and DIG strong-line ratio relations from SDSS-IV MaNGA IFU data. Flux-weighting effects and DIG contamination can significantly affect properties inferred from global galaxy spectra, biasing metallicity estimates by more than 0.3 dex in some cases. We use observationally-motivated inputs to construct a model matched to typical local star-forming galaxies, and quantify the biases in strong-line ratios, electron temperatures, and direct-method metallicities as inferred from global galaxy spectra relative to the median values of the HII region distributions in each galaxy. We also provide a generalized set of models that can be applied to individual galaxies or galaxy samples in atypical regions of parameter space. We use these models to correct for the effects of flux-weighting and DIG contamination in the local direct-method mass-metallicity and fundamental metallicity relations, and in the mass-metallicity relation based on strong-line metallicities. Future photoionization models of galaxy line emission need to include DIG emission and represent galaxies as ensembles of emitting regions with varying metallicity, instead of as single HII regions with effective properties, in order to obtain unbiased estimates of key underlying physical properties.
Telescope Array Hybrid Composition and Auger-TA Composition Comparison

Telescope Array (TA) has completed analysis of nearly nine years of data measuring the atmospheric depth of air shower maximum (Xmax ) utilizing the TA surface detector array and the Black Rock Mesa and Long Ridge fluorescence detector stations. By using both the surface array and the fluorescence detector, the geometry and arrival time of air showers can be measured very precisely providing good resolution in determining Xmax . Xmax is directly related to the air shower primary particle mass and is therefore important for understanding the composition of ultra high energy cosmic rays (UHECRs). UHECR composition will help answer questions such as the distance and location of their sources. We discuss the experimental apparatus, analysis method, and Xmax data collected. We compare the energy dependent distributions of the observed data to detailed Monte Carlo simulations of four chemical species, then test which individual species are not compatible with the data through an analysis of the shapes of the distributions. We also discuss the present state of composition analysis and interpretation between the Auger and TA experiments. These are the two largest UHECR observatories in the world with large exposures and should shed light on UHECR composition.
Highly tunable ultra-narrow-resonances with optical nano-antenna phased arrays in the infrared

We report our recent development in pursuing high Quality-Factor (high-Q factor) plasmonic resonances, with vertically aligned two dimensional (2-D) periodic nanorod arrays. The 2-D vertically aligned nano-antenna array can have high-Q resonances varying arbitrarily from near infrared to terahertz regime, as the antenna resonances of the nanorod are highly tunable through material properties, the length of the nanorod, and the orthogonal polarization direction with respect to the lattice surface,. The high-Q in combination with the small optical mode volume gives a very high Purcell factor, which could potentially be applied to various enhanced nonlinear photonics or optoelectronic devices. The 'hot spots' around the nanorods can be easily harvested as no index-matching is necessary. The resonances maintain their high-Q factor with the change of the environmental refractive index, which is of great interest for molecular sensing.
Polyurethane spray coating of aluminum wire bonds to prevent corrosion and suppress resonant oscillations

Unencapsulated aluminum wedge wire bonds are common in particle physics pixel and strip detectors. Industry-favored bulk encapsulation is eschewed due to the range of operating temperatures and radiation. Wire bond failures are a persistent source of tracking-detector failure. Unencapsulated bonds are vulnerable to condensation-induced corrosion, particularly when halides are present. Oscillations from periodic Lorentz forces are documented as another source of wire bond failure. Spray application of polyurethane coatings, performance of polyurethane-coated wire bonds after climate chamber exposure, and resonant properties of polyurethane-coated wire bonds and their resistance to periodic Lorentz forces are under study for use in a future High Luminosity Large Hadron Collider detector such as the ATLAS Inner Tracker upgrade.
Performance Limitations of Observer-Based Feedback for Transient Energy Growth Suppression

Transient energy growth suppression is a common control objective for feedback flow control aimed at delaying transition to turbulence. A prevailing control approach in this context is observer-bas...
On the distribution of the zeros of the derivative of the Riemann zeta-function

We establish an asymptotic formula describing the horizontal distribution of the zeros of the derivative of the Riemann zeta-function. For ℜ(s) = σ satisfying (log T)−1/3+e ⩽ (2σ − 1) ⩽ (log log T)−2, we show that the number of zeros of ζ′(s) with imaginary part between zero and T and real part larger than σ is asymptotic to T/(2π(σ−1/2)) as T → ∞. This agrees with a prediction from random matrix theory due to Mezzadri. Hence, for σ in this range the zeros of ζ′(s) are horizontally distributed like the zeros of the derivative of characteristic polynomials of random unitary matrices are radially distributed.
Energy flux through the horizon in the black hole-domain wall systems

We study various conflgurations in which a domain wall (or cosmic string), described by the Nambu-Goto action, is embedded in a background space-time of a black holein(3+1)andhigherdimensionalmodels. Wecalculateenergy∞uxesthroughtheblack holehorizon. Inthesimplestcase,whenastaticdomainwallentersthehorizonofastatic black hole perperdicularly, the energy ∞ux is zero. In more complicated situations, where parameters which describe the domain wall surface are time and position dependent, the ∞ux is non-vanishing is principle. These results are of importance in various conventional cosmological models which accommodate the existence of domain walls and strings and also inbraneworldscenarios.
The integration of three-dimensional Lotka–Volterra systems

The general solutions of many three-dimensional Lotka–Volterra systems, previously known to be at least partially integrable, are constructed with the aid of special functions. Examples include certain ABC and May–Leonard systems. The special functions used are elliptic and incomplete beta functions. In some cases, the solution is parametric, with the independent and dependent variables expressed as functions of a ‘new time’ variable. This auxiliary variable satisfies a nonlinear third-order differential equation of a generalized Schwarzian type, and results of Carton-LeBrun on the equations of this type that have the Painleve property are exploited, so as to produce solutions in closed form. For several especially difficult Lotka–Volterra systems, the solutions are expressed in terms of Painleve transcendents. An appendix on incomplete beta functions and closed-form expressions for their inverses is included.
Future colliders symposium in Hong Kong: Scientific overview

Opening Lecture at the Hong Kong University of Science and Technology Jockey Club Institute for Advanced Study Program on High Energy Physics Conference, January 18–21, 2016.
USING RED CLUMP STARS TO DECOMPOSE THE GALACTIC MAGNETIC FIELD WITH DISTANCE

A new method for measuring the large-scale structure of the Galactic magnetic field is presented. The Galactic magnetic field has been probed through the Galactic disk with near-infrared starlight polarimetry; however, the distance to each background star is unknown. Using red clump stars as near-infrared standard candles, this work presents the first attempt to decompose the line-of-sight structure of the sky-projected Galactic magnetic field. Two example lines of sight are decomposed: toward a field with many red clump stars and toward a field with few red clump stars. A continuous estimate of magnetic field orientation over several kiloparsecs of distance is possible in the field with many red clump stars, while only discrete estimates are possible in the sparse example. Toward the outer Galaxy, there is a continuous field orientation with distance that shows evidence of perturbation by the Galactic warp. Toward the inner Galaxy, evidence for a large-scale change in the magnetic field geometry is consistent with models of magnetic field reversals, independently derived from Faraday rotation studies. A photo-polarimetric method for identifying candidate intrinsically polarized stars is also presented. The future application of this method to large regions of the sky will begin the process of mapping the Galactic magnetic field in a way never before possible.
Low mass companions to white dwarfs

This paper summarizes the results of over 17 years of work searching for low mass stellar and substellar companions to more than 370 nearby white dwarfs. Roughly 60 low mass, unevolved companions were found and studied all together, with over 20 discovered in the last few years, including the first unambiguous brown dwarf companion to a white dwarf, GD 1400B. The resulting spectral type distributions for companions to white dwarfs and nearby cool field dwarfs are compared, and the implications for binary star formation are discussed. A brief analysis of GD 1400B, including new data, is also presented. (© 2005 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim)
TESS Reveals that the Nearby Pisces-Eridanus Stellar Stream is only 120 Myr Old

Pisces-Eridanus (Psc-Eri), a nearby ($d$ $\simeq$ 80-226 pc) stellar stream stretching across $\approx$120 degrees of the sky, was recently discovered with Gaia data. The stream was claimed to be $\approx$1 Gyr old, which would make it an exceptional discovery for stellar astrophysics, as star clusters of that age are rare and tend to be distant, limiting their utility as benchmark samples. We test this old age for Psc-Eri in two ways. First, we compare the rotation periods for 101 low-mass members (measured using time series photometry from the Transiting Exoplanet Survey Satellite, TESS) to those of well-studied open clusters. Second, we identify 34 new high-mass candidate members, including the notable stars $\lambda$ Tauri (an Algol-type eclipsing binary) and HD 1160 (host to a directly imaged object near the hydrogen-burning limit). We conduct an isochronal analysis of the color--magnitude data for these highest-mass members, again comparing our results to those for open clusters. Both analyses show that the stream has an age consistent with that of the Pleiades, i.e., $\approx$120 Myr. This makes the Psc-Eri stream an exciting source of young benchmarkable stars and, potentially, exoplanets located in a more diffuse environment that is distinct from that of the Pleiades and of other dense star clusters.
SEARCH FOR THE FOOTPRINTS OF NEW PHYSICS WITH LABORATORY AND COSMIC NEUTRINOS

Observations of high energy neutrinos, both in the laboratory and from cosmic sources, can be a useful probe in searching for new physics. Such observations can provide sensitive tests of Lorentz invariance violation (LIV), which may be a the result of quantum gravity physics (QG). We review some observationally testable consequences of LIV using effective field theory (EFT) formalism. To do this, one can postulate the existence of additional small LIV terms in free particle Lagrangians, suppressed by powers of the Planck mass. The observational consequences of such terms are then examined. In particular, one can place limits on a class of non-renormalizable, mass dimension five and six Lorentz invariance violating operators that may be the result of QG.
A CENSUS of YOUNG STARS and BROWN DWARFS in IC 348 and NGC 1333

We have obtained optical and near-infrared spectra of candidate members of the star-forming clusters IC 348 and NGC 1333. We classify 100 and 42 candidates as new members of the clusters, respectively, which brings the total numbers of known members to 478 and 203. We also have performed spectroscopy on a large majority of the previously known members of NGC 1333 in order to provide spectral classifications that are measured with the same scheme that has been applied to IC 348 in previous studies. The new census of members is nearly complete for Ks<16.8 at Aj<1.5 in IC 348 and for Ks<16.2 at Aj<3 in NGC 1333, which correspond to masses of <=0.01 Msun for ages of 3 Myr according to theoretical evolutionary models. The faintest known members extend below these completeness limits and appear to have masses of ~0.005 Msun. In extinction-limited samples of cluster members, NGC 1333 exhibits a higher abundance of objects at lower masses than IC 348. It would be surprising if the initial mass functions of these clusters differ significantly given their similar stellar densities and formation environments. Instead, it is possible that average extinctions are lower for less massive members of star-forming clusters, in which case extinction-limited samples could be biased in favor of low-mass objects in the more heavily embedded clusters like NGC 1333. In the H-R diagram, the median sequences of IC 348 and NGC 1333 coincide with each other for the adopted distances of 300 and 235 pc, which would suggest that they have similar ages. However, NGC 1333 is widely believed to be younger than IC 348 based on its higher abundance of disks and protostars and its greater obscuration. Errors in the adopted distances may be responsible for this discrepancy.
Another weak first order deconfinement transition: three-dimensional SU(5) gauge theory

We examine the finite-temperature deconfinement phase transition of (2+1)-dimensional SU(5) Yang-Mills theory via non-perturbative lattice simulations. Unsurprisingly, we find that the transition is of first order, however it appears to be weak. This fits naturally into the general picture of ``large'' gauge groups having a first order deconfinement transition, even when the center symmetry associated with the transition might suggest otherwise.
Distributed assignment with limited communication for multi-robot multi-target tracking

We study the problem of tracking multiple moving targets using a team of mobile robots. Each robot has a set of motion primitives to choose from in order to collectively maximize the number of targets tracked or the total quality of tracking. Our focus is on scenarios where communication is limited and the robots have limited time to share information with their neighbors. As a result, we seek distributed algorithms that can find solutions in a bounded amount of time. We present two algorithms: (1) a greedy algorithm that is guaranteed to find a 2-approximation to the optimal (centralized) solution but requiring |R| communication rounds in the worst case, where |R| denotes the number of robots, and (2) a local algorithm that finds a $$\mathcal {O}\left( (1+\epsilon )(1+1/h)\right) $$—approximation algorithm in $$\mathcal {O}(h\log 1/\epsilon )$$ communication rounds. Here, h and $$\epsilon $$ are parameters that allow the user to trade-off the solution quality with communication time. In addition to theoretical results, we present empirical evaluation including comparisons with centralized optimal solutions.