cssi/SciSciGPT-SciSciNet huggingface dataset:
Functional overexpression and characterization of lipogenesis-related genes in the oleaginous yeast Yarrowia lipolytica

Single cell oil (SCO) is an attractive energy source due to scalability, utilization of low-cost renewable feedstocks, and type of product(s) made. Engineering strains capable of producing high lipid titers and yields is crucial to the economic viability of these processes. However, lipid synthesis in cells is a complex phenomenon subject to multiple layers of regulation, making gene target identification a challenging task. In this study, we aimed to identify genes in the oleaginous yeast Yarrowia lipolytica whose overexpression enhances lipid production by this organism. To this end, we examined the effect of the overexpression of a set of 44 native genes on lipid production in Y. lipolytica, including those involved in glycerolipid synthesis, fatty acid synthesis, central carbon metabolism, NADPH generation, regulation, and metabolite transport and characterized each resulting strain's ability to produce lipids growing on both glucose and acetate as a sole carbon source. Our results suggest that a diverse subset of genes was effective at individually influencing lipid production in Y. lipolytica, sometimes in a substrate-dependent manner. The most productive strain on glucose overexpressed the diacylglycerol acyltransferase DGA2 gene, increasing lipid titer, cellular content, and yield by 236, 165, and 246 %, respectively, over our control strain. On acetate, our most productive strain overexpressed the acylglycerol-phosphate acyltransferase SLC1 gene, with a lipid titer, cellular content, and yield increase of 99, 91, and 151 %, respectively, over the control strain. Aside from genes encoding enzymes that directly catalyze the reactions of lipid synthesis, other ways by which lipogenesis was increased in these cells include overexpressing the glycerol-3-phosphate dehydrogenase (GPD1) gene to increase production of glycerol head groups and overexpressing the 6-phosphogluconolactonase (SOL3) gene from the oxidative pentose phosphate pathway to increase NADPH availability for fatty acid synthesis. Taken together, our study demonstrates that the overall kinetics of microbial lipid synthesis is sensitive to a wide variety of factors. Fully optimizing a strain for single cell oil processes could involve manipulating and balancing many of these factors, and, due to mechanistic differences by which each gene product investigated here impacts lipid synthesis, there is a high likelihood that many of these genes will work synergistically to further increase lipid production when simultaneously overexpressed.
National Institute of Standards and Technology measurement service of the optical properties of biomedical phantoms: Current status

The National Institute of Standards and Technology (NIST) has maintained scales for reflectance and transmittance over several decades. The scales are primarily intended for regular transmittance, mirrors, and solid surface scattering diffusers. The rapidly growing area of optical medical imaging needs a scale for volume scattering of diffuse materials that are used to mimic the optical properties of tissue. Such materials are used as phantoms to evaluate and validate instruments under development intended for clinical use. To address this need, a double-integrating sphere based instrument has been installed to measure the optical properties of tissue-mimicking phantoms. The basic system and methods have been described in previous papers. An important attribute in establishing a viable calibration service is the estimation of measurement uncertainties. The use of custom models and comparisons with other established scales enabled uncertainty measurements. Here, we describe the continuation of those efforts to advance the understanding of the uncertainties through two independent measurements: the bidirectional reflectance distribution function and the bidirectional transmittance distribution function of a commercially available solid biomedical phantom. A Monte Carlo-based model is used and the resulting optical properties are compared to the values provided by the phantom manufacturer.
Control of Elongation in Highly Stretched Cotton Tire Cord

Abstract 1. Cotton tire cords, differing with regard to gauge, construction, and variety of cotton, were subjected to stretching treatments involving various combinations of tension, heat, and moisture. It was found that all these treatments increased the strength of the cords but reduced their gauge and elongation at 10 pounds. The greatest increase in strength was obtained when tire cord was stretched in a swollen condition and in the presence of heat. Increases in count-strength product from 48 to 83 per cent were observed. 2. Experiments showed a reciprocal relationship between the strength and the elongation at 10 pounds obtainable by single-stretching treatments of tire cord, which makes impossible the control of elongation, independently of strength. Bone-dry elongations of about 6 per cent at 10 pounds could be obtained only with negligible increase in strength. 3. The original elongation was restored by treating highly stretched tire cord with water at room temperature for 30 minutes or with boil...
Cell-Based Biosensor to Report DNA Damage in Micro- and Nanosystems

Understanding how newly engineered micro- and nanoscale materials and systems that interact with cells impact cell physiology is crucial for the development and ultimate adoption of such technologies. Reports regarding the genotoxic impact of forces applied to cells in such systems that can both directly or indirectly damage DNA emphasize the need for developing facile methods to assess how materials and technologies affect cell physiology. To address this need we have developed a TurboRFP-based DNA damage reporter cell line in NIH-3T3 cells that fluoresce to report genotoxic stress caused by a wide variety of agents, from chemical genotoxic agents to UV-C radiation. Our biosensor was successfully implemented in reporting the genotoxic impact of nanomaterials, demonstrating the ability to assess size dependent geno- and cyto-toxicity. The biosensor cells can be assayed in a high throughput, noninvasive manner, with no need for overly sophisticated equipment or additional reagents. We believe that this open-source biosensor is an important resource for the community of micro- and nanomaterials and systems designers and users who wish to evaluate the impact of systems and materials on cell physiology.
Fifty years of studies on human evolution

The Bulletin's prevailing concern is with dangers to human well being and even survival that have scientific-technological roots or ingredients and seldom any self-evident solutions. By implication, scientific research itself may sometimes be projected more as threat than promise. At the same time, current legislative challenges to the teaching of evolutionary science by “creation scientists” may indicate a lack of widespread public understanding of the difference between the creed of science and other kinds of creeds. Professor Sherwood L. Washburn speaks indirectly, but eloquently to both of these issues.It is difficult for non-specialists to form an impression of how, and how much, progress occurs in most scientific research. The overall pace of the advance is easily obscured by multiplying new discoveries, new questions and new methods. Among them often are false leads that for a time set unproductive directions. To convey the zigzag path of accomplishment across decades as a vivid, intelligible patte...
Fulfill Your Digital Preservation Goals with a Budget Studio

In order to fulfill digital preservation goals, many institutions use high-end scanners for in-house scanning of historical print and oversize materials. However, high-end scanners’ prices do not fit in many small institutions’ budget. As digital single-lens reflex (DSLR) camera technologies advance and camera prices drop quickly, a budget photography studio can help to achieve institutions’ preservation goals. This paper compares images delivered by a high-end overhead scanner and a consumer level DSLR camera, discusses pros and cons of using each method, demonstrates how to set up a cost efficient shooting studio, and presents a budget estimate for a studio.
Tunable single-mode fiber reflective grating filter

By placing a periodic perturbation in the evanescent field of a side-pollshed single-mode fiber,1–4 a narrowband reflection filter can be constructed.2,3 These fiber-compatible devices offer the potential for high efficiency3 and low insertion loss, since the signal is not removed from the fiber. One limitation of these previously demonstrated devices2,3 Is that they operate at only one fixed wavelength which Is set by the spatial period of the evanescent perturbation. We describe a method which allows for tunable operation of a narrowband evanescent-field reflection filter.
Simulation of optical response functions in molecular junctions

We discuss theoretical approaches to nonlinear optical spectroscopy of molecular junctions. Optical response functions are derived in a form convenient for the implementation of Green function techniques, and their expressions in terms of pseudoparticle nonequilibrium Green functions are proposed. The formulation allows to account for both intramolecular interactions and hybridization of molecular states with those of contacts. Within a generic model and utilizing two-dimensional optical spectroscopy as an example, the methodology is compared with exact simulations and is shown to work where the traditional Liouville space approach fails.
An Edge-Based Formulation for Combined-Cycle Units

As the number of combined-cycle units increases, efficient modeling approaches for these units play important roles for independent system operators (ISOs). Based on various combinations of combustion turbines (CTs) and steam turbines (STs), the combined-cycle unit could work at different configurations (modes) with different efficiencies. In this paper, we propose an edge-based formulation for the combined-cycle units in the unit commitment problem to improve the accuracy and effectiveness of current modeling approaches. Our formulation can 1) clearly describe the transition processes among different configurations so as to satisfy the ISO financial offer submission requirements and (2) capture physical constraints of each turbine, including the exact min-up/down time and time dependent startup cost, in the combined-cycle units so as to increase the operational flexibility while ensuring system feasibility. This model fits well with the current U.S. deregulated electricity market. The final numerical studies show that our approaches perform better than the current configuration-based modeling approach.
Multi-Eulerian Tours of Directed Graphs

Not every graph has an Eulerian tour. But every finite, strongly connected graph has a multi-Eulerian tour, which we define as a closed path that uses each directed edge at least once, and uses edges e and f the same number of times whenever tail(e)=tail(f). This definition leads to a simple generalization of the BEST Theorem. We then show that the minimal length of a multi-Eulerian tour is bounded in terms of the Pham index, a measure of 'Eulerianness'.
Tinea capitis: diagnostic criteria and treatment options.

Tinea capitis is a fungal infection involving the hair shaft of the scalp. It is commonly referred to as ringworm and occurs primarily in children. Treatment with a systemic anti-fungal rather than topical treatment is required. Currently, two medications, griseofulvin (Grifulvin®) and terbinafine (Lamisil Granules®), are FDA-approved to treat tinea capitis. Treatment with griseofulvin is usually 6 to 8 weeks, while treatment with terbinafine requires 6 weeks. There are other medications currently not FDA-approved to treat tinea capitis that have similar cure rates and shorter durations of treatment for tinea capitis, and as a result, are being used off-label. This article reviews the research-based literature related to the treatment of tinea capitis with various pharmacologic agents.
Development of one-cell porcine embryos in two culture systems.

The effect of culture system and protein supplementation on the development of one-cell porcine embryos was investigated. One hundred and sixty-four one-cell embryos were collected at slaughter from 19 handmated gifts. Culture systems evaluated were microdrops of Whitten's medium (WM) under paraffin oil (M) or tubes with 4.0 ml of WM (T). Also tested was T with a 2.0 ml paraffin oil overlay (O). Media evaluated were WM with: no bovine serum albumin (-BSA), 15 mg/ml BSA (+BSA) or 10% (v/v) heat-treated porcine serum (+HTPS). Twenty-nine, 29, 28, 29, 28 and 21 one-cell embryos were assigned to treatments T + BSA + O, T - BSA, M + BSA, M - BSA and M + HTPS, respectively. All cultures were conducted at 37 C in a humidified atmosphere of 5% CO2 in air. At the cessation of division, embryos were fixed and stained, and each was assigned a cleavage index bases on the number of divisions completely in culture. The mean cleavate indexes for embryos cultured in T + BSA + O (2.07) and T + BSA (1.97) were not significantly different, but both were greater (P less than .05) than the indexes for T - BSA (1.09), M + BSA (1.12), M - BSA (.82) and M + HTPS (.86). Mean cleavage indexes for embryos cultured in T - BSA, M + BSA, M - BSA and M + HTPS were not significantly different. More (P less than .05) embryos developed to the blastocyst stage in T + BSA + O (6/29) than in either T - BSa (0.28) or M BSA (0.28). Fragmentation was greater (P less than .05) in embryos cultured in M - BSA than in embryos cultured in tubes. These results suggest that culture tubes of WM with 1.5% BSA are superior to microdrops and WM with 10% HTPS in supporting the in vitro development of one-cell porcine embryos.
Cutting out the middleman : Measuring nuclear area in histopathology slides without segmentation

The size of nuclei in histological preparations from excised breast tumors is predictive of patient outcome (large nuclei indicate poor outcome). Pathologists take into account nuclear size when performing breast cancer grading. In addition, the mean nuclear area (MNA) has been shown to have independent prognostic value. The straightforward approach to measuring nuclear size is by performing nuclei segmentation. We hypothesize that given an image of a tumor region with known nuclei locations, the area of the individual nuclei and region statistics such as the MNA can be reliably computed directly from the image data by employing a machine learning model, without the intermediate step of nuclei segmentation. Towards this goal, we train a deep convolutional neural network model that is applied locally at each nucleus location, and can reliably measure the area of the individual nuclei and the MNA. Furthermore, we show how such an approach can be extended to perform combined nuclei detection and measurement, which is reminiscent of granulometry.
IMPLEMENTATION AND CHARACTERIZATION OF A FLEXURE-BEAM MICROMECHANICAL SPATIAL LIGHT MODULATOR

The phase-only spatial light modulator (SLM) is a highly efficient component for the filter plane of a real-time autocorrelator.'3 Texas Instruments has developed several SLMs using micromechanical mirror elements.4 The basic structure of the flexure-beam micromechanical element that we implement in this research is shown in Fig. 1 .Themirror element consists of a square reflecting plate attached at four points to L-shaped flexure hinges. The hinges are attached to four posts that provide the main mechanical support and electrical contact for the element. Each post also mechanically supports four hinges that attach to four different mirrors. The pixel is attracted downward by electrostatic force when it is addressed. The vertical motion of the mirror changes the length of the optical path at the pixel and hence the phase information. There are two approaches to building such a micromirror device: (1) addressing at the mirror through the post and hinge, or (2) addressing at the bottom electrode of the spacer. The advantage of using the first approach is the reduction of capacitance feedthrough caused by a nearby underlayer that carries signals. This approach has a smaller active optical area, because a larger post is needed to provide an electrical signal on one hinge while isolating the signal from the three others. Our chip uses the first approach. The next two sections briefly describe the chip architecture and process flow with a cross section of the flexure-beam micromirror device. The fourth section illustrates the modeling effort for this device. The fifth section then summarizes the characterization and performance of the device.
Solution 31P NMR Study of the Acid-Catalyzed Formation of a Highly Charged {U24Pp12} Nanocluster, [(UO2)24(O2)24(P2O7)12]48–, and Its Structural Characterization in the Solid State Using Single-Crystal Neutron Diffraction

The first neutron diffraction study of a single crystal containing uranyl peroxide nanoclusters is reported for pyrophosphate-functionalized Na44K6[(UO2)24(O2)24(P2O7)12][IO3]2·140H2O (1). Relative to earlier X-ray studies, neutron diffraction provides superior information concerning the positions of H atoms and lighter counterions. Hydrogen positions have been assigned and reveal an extensive network of H-bonds; notably, most O atoms present in the anionic cluster accept H-bonds from surrounding H2O molecules, and none of the surface-bound O atoms are protonated. The D4h symmetry of the cage is consistent with the presence of six encapsulated K cations, which appear to stabilize the lower symmetry variant of this cluster. 31P NMR measurements demonstrate retention of this symmetry in solution, while in situ 31P NMR studies suggest an acid-catalyzed mechanism for the assembly of 1 across a wide range of pH values.
The Effect of Local Tournament Incentives on Firms' Performance, Risk-Taking Decisions, and Financial Reporting Decisions

ABSTRACT This study documents the existence of local employment preferences for corporate executives and examines how the compensation of executives' local peers affects their own performance, risk...
Morphological and nanomechanical analyses of ground tire rubber-modified asphalts

Automobile industries produce more than 5.2 million tons of scrapped tires each year in the United States. Disposal of such a huge amount of waste scrapped tires has become a serious environmental issue. Scopes to use scrapped tires in the form of Ground Tire Rubber (GTR) in pavement industry have been analyzed in recent years. The GTR has potential to improve hot mix asphalt’s performance from the view points of stiffness, resilience and shock absorbance properties. On the other hand, in recent years, researchers have attempted to explain performance of asphalt in terms of its nanomechanical characteristics. In this study, the PeakForce Quantitative Nanomechanical Mapping (PFQNM™) mode of an atomic force microscope has been employed to find basic nanomechanistic properties and the morphology of GTR-modified asphalt binders. A performance grade (PG) binder (PG 64-22) modified with two different grades of GTR (Mesh #30 and Mesh #40) samples have been evaluated in this study. Nanomechanical properties such as adhesion, energy dissipation, deformation, and DMT (Derjaguin, Muller, and Toporov) modulus for the GTR-modified binders have been quantified. Each sample was scanned for three different (5 × 5, 10 × 10, and 20 × 20 µm) areas. The PFQNM™ analyses revealed distinct microstructures and grain distributions among tested additive modified binder samples. Two distinct phases, namely Catana and Peri-phase, were observed in GTR-modified samples, although the DMT moduli were found to be in a close range in these areas. The neat binder showed another phase, named Perpetua, which was missing from the GTR-modified samples. It was observed that modification of asphalt by addition of GTR considerably changes the mechanistic properties of the base binder.
Glycosylation via Transition‐Metal Catalysis: Challenges and Opportunities

Development of efficient, mild, and easily operable stereoselective glycosylations is of critical importance to access sufficient amounts of pure and structurally well-defined carbohydrates for studies of their biological functions. Such studies will facilitate our understanding of the role of complex oligosaccharides and glycoconjugates in biological processes as well as the development of carbohydrate-based effective therapeutic agents. This review highlights recent advances in the transition metal catalyzed stereoselective glycosylations for the synthesis of a variety of structurally complex and biologically significant O-, N-, C-, and S-glycosides.
The European Macroeconomy

This chapter looks at a series of tests of macroeconomic influences that run across national boundaries. Of course it is indisputable that the industrial revolution spilled across state lines, but whether the effects were broad enough to produce an interaction that can be discerned by means of macroeconomic time-series tests is certainly another matter. Indeed, because most of the formal tests proposed here require that the relationship hold up for a considerable time, the cards seem stacked against the general hypothesis. Even so, there are good reasons to believe that growth was an interactive process in Europe at this time, perhaps because of spillovers and perhaps because of the possibly increasingly pan-European nature of capital markets (and business cycles). Of course the adoption of the gold standard in this period by the countries covered in this study also increases the likelihood of there being discernible ties, particularly of financial variables.
Lattice Methods and Effective Field Theory

Lattice field theory is a non-perturbative tool for studying properties of strongly interacting field theories, which is particularly amenable to numerical calculations and has quantifiable systematic errors. In these lectures we apply these techniques to nuclear Effective Field Theory (EFT), a non-relativistic theory for nuclei involving the nucleons as the basic degrees of freedom. The lattice formulation of Endres et al. (Phys Rev A 84:043644, 2011; Phys Rev A 87:023615, 2013) for so-called pionless EFT is discussed in detail, with portions of code included to aid the reader in code development. Systematic and statistical uncertainties of these methods are discussed at length, and extensions beyond pionless EFT are introduced in the final section.
Smoke screen: Estimating the tax pass‐through to cigarette prices in Pakistan

This article estimates and compares the speed and magnitude of the tax pass‐through across major cigarette brands at different price points (budget, mainstream, and premium) in Pakistan by using a novel dataset of monthly observations on cigarette prices in 50 cities during the period 2004 to 2015. The empirical analysis indicates that the pass‐through of cigarette taxes to the final consumer price is fast but incomplete in Pakistan. The pass‐through coefficient is estimated to be in the range of 70 to over 90 percent across four major cigarette brands, and most of the pass‐through occurs contemporaneously within a period of 2 months. The results imply that a 1‐Pakistan rupee (PR) increase in taxation leads to an increase of PRs 0.8, on average, in cigarette prices. In other words, cigarette taxes are undershifted to consumers in Pakistan. With respect to the tax pass‐through at different price tiers (budget, mainstream, and premium), I find significant variation in the pass‐through coefficient, which is close to one for the premium cigarette brand and significantly lower for the budget and mainstream cigarette brands.
Local Heat Transfer to Staggered Arrays of Impinging Circular Air Jets

Measurements are made of the local heat transfer from a flat plate to arrays of impinging circular air jets. Fluid from the spent jets is constrained to flow out of the system in one direction. Two different jet-to-jet spacings, 4 and 8 jet diameters, are employed. The parameters that are varied include jet-orifice-plate to impingement-surface spacing and jet Reynolds number. Local heat transfer coefficients vary periodically both in the flow direction and across the span with high values occurring in stagnation regions. Stagnation regions of individual jets as determined by local heat transfer coefficients move further in the downstream direction as the amount of crossflow due to upstream jet air increases. Local heat transfer coefficients are averaged numerically to obtain spanwise and streamwise-spanwise averaged heat transfer coefficients.
Reference fiction, and omission

In this paper, I argue that sentences that contain ‘omission’ tokens that appear to function as singular terms are meaningful while maintaining the view that omissions are nothing at all or mere absences. I take omissions to be fictional entities and claim that the way in which sentences about fictional characters are true parallels the way in which sentences about omissions are true. I develop a pragmatic account of fictional reference and argue that my fictionalist account of omissions implies a plausible account of the metaphysics of omissions.
Minimum node degree in inhomogeneous random key graphs with unreliable links

We consider wireless sensor networks under a heterogeneous random key predistribution scheme and an on-off channel model. The heterogeneous key predistribution scheme has recently been introduced by Yagan - as an extension to the Eschenauer and Gligor scheme - for the cases when the network consists of sensor nodes with varying level of resources and/or connectivity requirements, e.g., regular nodes vs. cluster heads. The network is modeled by the intersection of the inhomogeneous random key graph (induced by the heterogeneous scheme) with an Erdős-Renyi graph (induced by the on/off channel model). We present conditions (in the form of zero-one laws) on how to scale the parameters of the intersection model so that with high probability all of its nodes are connected to at least k other nodes; i.e., the minimum node degree of the graph is no less than k. We also present numerical results to support our results in the finite-node regime. The numerical results suggest that the conditions that ensure k-connectivity coincide with those ensuring the minimum node degree being no less than k.
Inhaled nitric oxide therapy for pulmonary disorders of the term and preterm infant

The 21st century began with the FDA approval of inhaled nitric oxide therapy for the treatment of neonatal hypoxic respiratory failure associated with pulmonary hypertension in recognition of the 2 randomized clinical trials demostrating a significant reduction in the need for extracorporeal support in the term and near-term infant. Inhaled nitric oxide is one of only a few therapeutic agents approved for use through clinical investigations primarily in the neonate. This article provides an overview of the pertinent biology and chemistry of nitric oxide, discusses potential toxicities, and reviews the results of pertinent clinical investigations and large randomized clinical trials including neurodevelopmental follow-up in term and preterm neonates. The clinical investigations conducted by the Eunice Kennedy Shriver NICHD Neonatal Research Network will be discussed and placed in context with other pertinent clinical investigations exploring the efficacy of inhaled nitric oxide therapy in neonatal hypoxic respiratory failure.
Legal access to alcohol and criminality

Previous research has found strong evidence that legal access to alcohol is associated with sizable increases in criminality. We revisit this relationship using the census of judicial records on criminal charges filed in Oregon Courts, the ability to separately track crimes involving firearms, and to track individuals over time. We find that crime increases at age 21, with increases mostly due to assaults that lack premeditation, and alcohol-related nuisance crimes. We find no evident increases in rape or robbery. Among those with no prior criminal records, increases in crime are 50% larger-still larger for the most socially costly crimes of assault and drunk driving.
A neural network alternative to non-negative audio models

We present a neural network that can act as an equivalent to a Non-Negative Matrix Factorization (NMF), and further show how it can be used to perform supervised source separation. Due to the extensibility of this approach we show how we can achieve better source separation performance as compared to NMF-based methods, and propose a variety of derivative architectures that can be used for further improvements.
How Efficiently Can One Untangle a Double-Twist? Waving is Believing!

It has long been known to mathematicians and physicists that while a full rotation in three-dimensional Euclidean space causes tangling, two rotations can be untangled. Formally, an untangling is a based nullhomotopy of the double-twist loop in the special orthogonal group of rotations. We study a particularly simple, geometrically defined untangling procedure, leading to new conclusions regarding the minimum possible complexity of untanglings. We animate and analyze how our untangling operates on frames in 3-space, and teach readers in a video how to wave the nullhomotopy with their hands.
Structured Group Sparsity: A Novel Indoor WLAN Localization, Outlier Detection, and Radio Map Interpolation Scheme

This paper introduces novel schemes for indoor localization, outlier detection, and radio map interpolation using wireless local area networks. The localization method consists of a novel multicomponent optimization technique that minimizes the squared $\ell _{2}$ -norm of the residuals between the radio map and the online received signal strength (RSS) measurements, the $\ell _{1}$ -norm of the user's location vector, and weighted $\ell _{2}$ -norms of layered groups of reference points (RPs). RPs are grouped using a new criterion based on the similarity between the so-called access point (AP) coverage vectors. In addition, since AP readings are prone to containing inordinate readings, called outliers, an augmented optimization problem is proposed to detect the outliers and localize the user with cleaned online measurements. Moreover, a novel scheme to record fingerprints from a smaller number of RPs and estimate the radio map at RPs without recorded fingerprints is developed using sparse recovery techniques. All localization schemes are tested on RSS fingerprints collected from a real environment. The overall scheme has comparable complexity with competing approaches, while it performs with high accuracy under a small number of APs and finer granularity of RPs.
The S.V.D. of the Poisson Kernel

The solution of the Dirichlet problem for the Laplacian on bounded regions $$\Omega $$ in $${\mathbb R}^{N}, \ N \ge 2$$ is generally described via a boundary integral operator with the Poisson kernel. Under mild regularity conditions on the boundary, this operator is a compact linear transformation of $$L^2 (\partial \Omega ,d \sigma )$$ to $$L^2_H(\Omega )$$ —the Bergman space of $$L^2$$ -harmonic functions on $$\Omega $$ . This paper describes the singular value decomposition of this operator and related results. The singular functions and singular values are constructed using Steklov eigenvalues and eigenfunctions of the biharmonic operator on $$\Omega $$ . These allow a spectral representation of the Bergman harmonic projection and the identification of an orthonormal basis of the real harmonic Bergman space $$L^2_H(\Omega )$$ . A reproducing kernel for $$L^2_H(\Omega )$$ and an orthonormal basis of the space $$L^2 (\partial \Omega ,d \sigma )$$ also are found. This enables the description of optimal finite rank approximations of the Poisson kernel with error estimates. Explicit spectral formulae for the normal derivatives of eigenfunctions for the Dirichlet Laplacian on $$\partial \Omega $$ are obtained and used to identify a constant in an inequality of Hassell and Tao.
Variational boosting: Iteratively refining posterior approximations

We propose a black-box variational inference method to approximate intractable distributions with an increasingly rich approximating class. Our method, termed variational boosting, iteratively refines an existing variational approximation by solving a sequence of optimization problems, allowing the practitioner to trade computation time for accuracy. We show how to expand the variational approximating class by incorporating additional covariance structure and by introducing new components to form a mixture. We apply variational boosting to synthetic and real statistical models, and show that resulting posterior inferences compare favorably to existing posterior approximation algorithms in both accuracy and efficiency.
Multilateral Trade Bargaining and Dominant Strategies

Motivated by GATT bargaining behavior and renegotiation rules, we construct a three-country, two-good general-equilibrium model of trade and examine multilateral tariff bargaining under the constraints of non-discrimination and multilateral reciprocity. We allow for a general family of government preferences and identify bargaining outcomes that can be implemented using dominant strategy proposals for all countries. In the implementation, tariff proposals are followed by multilateral rebalancing, a sequence that is broadly consistent with observed patterns identified by Bagwell, Staiger and Yurukoglu (2016) in the bargaining records for the GATT Torquay Round. The resulting bargaining outcome is efficient relative to government preferences if and only if the initial tariff vectors position the initial world price at its "politically optimal" level. In symmetric settings, if the initial tariffs correspond to Nash tariffs, then the resulting bargaining outcome is efficient and ensures greater-than-Nash trade volumes and welfares for all countries. We also highlight relationships between our work and previous research that examines strategy-proof rationing rules in other economic settings.
Directed Protein Packaging within Outer Membrane Vesicles from Escherichia coli: Design, Production and Purification

An increasing interest in applying synthetic biology techniques to program outer membrane vesicles (OMV) are leading to some very interesting and unique applications for OMV where traditional nanoparticles are proving too difficult to synthesize. To date, all Gram-negative bacteria have been shown to produce OMV demonstrating packaging of a variety of cargo that includes small molecules, peptides, proteins and genetic material. Based on their diverse cargo, OMV are implicated in many biological processes ranging from cell-cell communication to gene transfer and delivery of virulence factors depending upon which bacteria are producing the OMV. Only recently have bacterial OMV become accessible for use across a wide range of applications through the development of techniques to control and direct packaging of recombinant proteins into OMV. This protocol describes a method for the production, purification, and use of enzyme packaged OMV providing for improved overall production of recombinant enzyme, increased vesiculation, and enhanced enzyme stability. Successful utilization of this protocol will result in the creation of a bacterial strain that simultaneously produces a recombinant protein and directs it for OMV encapsulation through creating a synthetic linkage between the recombinant protein and an outer membrane anchor protein. This protocol also details methods for isolating OMV from bacterial cultures as well as proper handling techniques and things to consider when adapting this protocol for use for other unique applications such as: pharmaceutical drug delivery, medical diagnostics, and environmental remediation.
MESL: Proposal for a Non-volatile Cascadable Magneto-Electric Spin Logic

In the quest for novel, scalable and energy-efficient computing technologies, many non-charge based logic devices are being explored. Recent advances in multi-ferroic materials have paved the way for electric field induced low energy and fast switching of nano-magnets using the magneto-electric (ME) effect. In this paper, we propose a voltage driven logic-device based on the ME induced switching of nano-magnets. We further demonstrate that the proposed logic-device, which exhibits decoupled read and write paths, can be used to construct a complete logic family including XNOR, NAND and NOR gates. The proposed logic family shows good scalability with a quadratic dependence of switching energy with respect to the switching voltage. Further, the proposed logic-device has better robustness against the effect of thermal noise as compared to the conventional current driven switching of nano-magnets. A device-to-circuit level coupled simulation framework, including magnetization dynamics and electron transport model, has been developed for analyzing the present proposal. Using our simulation framework, we present energy and delay results for the proposed Magneto-Electric Spin Logic (MESL) gates.
Modeling Human Population Separation History Using Physically Phased Genomes

Phased haplotype sequences are a key component in many population genetic analyses since variation in haplotypes reflects the action of recombination, selection, and changes in population size. In humans, haplotypes are typically estimated from unphased sequence or genotyping data using statistical models applied to large reference panels. To assess the importance of correct haplotype phase on population history inference, we performed fosmid pool sequencing and resolved phased haplotypes of five individuals from diverse African populations (including Yoruba, Esan, Gambia, Maasai, and Mende). We physically phased 98% of heterozygous SNPs into haplotype-resolved blocks, obtaining a block N50 of 1 Mbp. We combined these data with additional phased genomes from San, Mbuti, Gujarati, and Centre de'Etude du Polymorphism Humain European populations and analyzed population size and separation history using the pairwise sequentially Markovian coalescent and multiple sequentially Markovian coalescent models. We find that statistically phased haplotypes yield a more recent split-time estimation compared with experimentally phased haplotypes. To better interpret patterns of cross-population coalescence, we implemented an approximate Bayesian computation approach to estimate population split times and migration rates by fitting the distribution of coalescent times inferred between two haplotypes, one from each population, to a standard isolation-with-migration model. We inferred that the separation between hunter-gatherer populations and other populations happened ∼120-140 KYA, with gene flow continuing until 30-40 KYA; separation between west-African and out-of-African populations happened ∼70-80 KYA; while the separation between Maasai and out-of-African populations happened ∼50 KYA.
The experiences of family members in the nursing home to hospital transfer decision

The objective of this study was to better understand the experiences of family members in the nursing home to hospital transfer decision making process. Semi-structured interviews were conducted with 20 family members who had recently been involved in a nursing home to hospital transfer decision. Family members perceived themselves to play an advocacy role in their resident’s care and interview themes clustered within three over-arching categories: Family perception of the nursing home’s capacity to provide medical care: Resident and family choices; and issues at ‘hand-off’ and the hospital. Multiple sub-themes were also identified. Findings from this study contribute to knowledge surrounding the nursing home transfer decision by illuminating the experiences of family members in the transfer decision process.
Long term regularity of the one-fluid Euler–Maxwell system in 3D with vorticity

Abstract A basic model for describing plasma dynamics is given by the “one-fluid” Euler–Maxwell system, in which a compressible electron fluid interacts with its own self-consistent electromagnetic field. In this paper we prove long-term regularity of solutions of this system in 3 spatial dimensions, in the case of small initial data with nontrivial vorticity. Our main conclusion is that the time of existence of solutions depends only on the size of the vorticity of the initial data, as long as the initial data is sufficiently close to a constant stationary solution.
Estimating recreation benefits through joint estimation of revealed and stated preference discrete choice data

We develop econometric models to estimate jointly revealed preference (RP) and stated preference (SP) models of recreational fishing behavior and preferences using survey data from the 2007 Alaska Saltwater Sportfishing Economic Survey. The RP data are from site choice survey questions, and the SP data are from a discrete choice experiment. Random utility models using only the RP data may be more likely to estimate the effect of cost on site selection well, but catch per day estimates may not reflect the benefits of the trip as perceived by anglers. The SP models may be more likely to estimate the effects of trip characteristics well, but less attention may be paid to the cost variable due to the hypothetical nature of the SP questions. The combination and joint estimation of RP and SP data seeks to exploit the contrasting strengths of both. We find that there are significant gains in econometric efficiency and differences between RP and SP willingness-to-pay estimates are mitigated by joint estimation. We compare a number of models that have appeared in the environmental economics literature with the generalized multinomial logit model. Naive (1) scaled, (2) mixed logit, and (3) generalized multinomial logit models produced similar results to a generalized multinomial logit model that accounts for scale differences in RP and SP data. Willingness-to-pay estimates do not differ across these models but are greater than those in the mixed logit error components model that accounts for scale differences.
Motif clustering and overlapping clustering for social network analysis

Motivated by applications in social network community analysis, we introduce a new clustering paradigm termed motif clustering. Unlike classical clustering, motif clustering aims to minimize the number of clustering errors associated with both edges and certain higher order graph structures (motifs) that represent “atomic units” of social organizations. Our contributions are two-fold: We first introduce motif correlation clustering, in which the goal is to agnostically partition the vertices of a weighted complete graph so that certain predetermined “important” social subgraphs mostly lie within the same cluster, while “less relevant” social subgraphs are allowed to lie across clusters. We then proceed to introduce the notion of motif covers, in which the goal is to cover the vertices of motifs via the smallest number of (near) cliques in the graph. Motif cover algorithms provide a natural solution for overlapping clustering and they also play an important role in latent feature inference of networks. For both motif correlation clustering and its extension introduced via the covering problem, we provide hardness results, algorithmic solutions and community detection results for two well-studied social networks.
Informational Substitutes

We propose definitions of substitutes and complements for pieces of information ("signals") in the context of a decision or optimization problem, with game-theoretic and algorithmic applications. In a game-theoretic context, substitutes capture diminishing marginal value of information to a rational decision maker. There, we address the main open problem in a fundamental strategic-information-revelation setting, prediction markets. We show that substitutes characterize "best-possible" equilibria with immediate information aggregation, while complements characterize "worst-possible", delayed aggregation. Game-theoretic applications also include settings such as crowdsourcing contests and question-and-answer forums. In an algorithmic context, where substitutes capture diminishing marginal improvement of information to an optimization problem, substitutes imply efficient approximation algorithms for a very general class of (adaptive) information acquisition problems. In tandem with these broad applications, we examine the structure and design of informational substitutes and complements. They have equivalent, intuitive definitions from disparate perspectives: submodularity, geometry, and information theory. We also consider the design of scoring rules or optimization problems so as to encourage substitutability or complementarity, with positive and negative results. Taken as a whole, the results give some evidence that, in parallel with substitutable items, informational substitutes play a natural conceptual and formal role in game theory and algorithms.
High performance distributed Bragg reflector microwave resonator

A new resonator device structure is described that achieves Q-factors well above those currently realizable for conventional room temperature microwave structures. The new structure consists of a microwave cavity, for which the enclosure walls consist of distributed Bragg reflectors (DBR) made of low-loss sapphire. For this configuration, most of the resonant field resides in empty space, with small field strengths in the thin layers of sapphire which comprise the DBR structure. The physical structure takes the form of interpenetrating concentric rings and plates of low-loss sapphire contained in a cylindrical metal enclosure. The theoretical analysis of the DBR resonant structure allows the positions and dimensions of the component rings and plates to be precisely determined for a specified resonant frequency. The resonator Q can be accurately calculated, and plots of the resonant fields clearly show the physical mechanism leading to the observed efficiency of this resonator structure. Experimental results are given for resonators designed at 9.0 and 13.2 GHz. The measured unloaded Q's at room temperature are over 650000 and 450000, respectively.
Adaptive 360 VR Video Streaming Based on MPEG-DASH SRD

We demonstrate an adaptive bandwidth-efficient 360 VR video streaming system based on MPEG-DASH SRD. We extend MPEG-DASH SRD to the 3D space of 360 VR videos, and showcase a dynamic view-aware adaptation technique to tackle the high bandwidth demands of streaming 360 VR videos to wireless VR headsets. We spatially partition the underlying 3D mesh into multiple 3D sub-meshes, and construct an efficient 3D geometry mesh called hexaface sphere to optimally represent tiled 360 VR videos in the 3D space. We then spatially divide the 360 videos into multiple tiles while encoding and packaging, use MPEG-DASH SRD to describe the spatial relationship of tiles in the 3D space, and prioritize the tiles in the Field of View (FoV) for view-aware adaptation. Our initial evaluation results show that we can save up to 72% of the required bandwidth on 360 VR video streaming with minor negative quality impacts compared to the baseline scenario when no adaptations is applied.