cssi/SciSciGPT-SciSciNet huggingface dataset:
Optogenetic regulation of site-specific subtelomeric DNA methylation

// Samrat Roy Choudhury 1 , Yi Cui 1 , Anoop Narayanan 2 , David P. Gilley 3 , Nazmul Huda 3 , Chiao-Ling Lo 4 , Feng C. Zhou 4, 5 , Dinesh Yernool 2 , Joseph Irudayaraj 1 1 Department of Agricultural & Biological Engineering, Bindley Bioscience Center, Purdue Center for Cancer Research, Purdue University, West Lafayette, IN 47907, USA 2 Bindley Laboratory of Structural Biology, Bindley Bioscience Center, Purdue University, West Lafayette, IN 47907, USA 3 Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, USA 4 Department of Anatomy and Cell Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA 5 Stark Institute of Neuroscience Research, Indiana University School of Medicine, Indianapolis, IN 46202, USA Correspondence to: Dinesh Yernool, email: dyernool@purdue.edu Joseph Irudayaraj, email: josephi@purdue.edu Keywords: optogenetics, single-cells tools, subtelomeric DNA-methylation, telomere-elongation Received: April 25, 2016 Accepted: June 18, 2016 Published: July 04, 2016 ABSTRACT Telomere length homeostasis, critical for chromosomal integrity and genome stability, is controlled by intricate molecular regulatory machinery that includes epigenetic modifications. Here, we examine site-specific and spatiotemporal alteration of the subtelomeric methylation of CpG islands using optogenetic tools to understand the epigenetic regulatory mechanisms of telomere length maintenance. Human DNA methyltransferase3A (DNMT3A) were assembled selectively at chromosome ends by fusion to cryptochrome 2 protein (CRY2) and its interacting complement, the basic helix loop helix protein-1 (CIB1). CIB1 was fused to the telomere-associated protein telomere repeat binding factor-1 (TRF1), which localized the protein complex DNMT3A-CRY2 at telomeric regions upon excitation by blue-light monitored by single-molecule fluorescence analyses. Increased methylation was achieved selectively at subtelomeric CpG sites on the six examined chromosome ends specifically after blue-light activation, which resulted in progressive increase in telomere length over three generations of HeLa cell replications. The modular design of the fusion constructs presented here allows for the selective substitution of other chromatin modifying enzymes and for loci-specific targeting to regulate the epigenetic pathways at telomeres and other selected genomic regions of interest.
Epidermal growth factor

During the course of purifying nerve growth factor from the submaxillary gland of the mouse, Cohen (1960) and Levi-Montalcini and Cohen (1960) noticed that daily injections of certain gland extract fractions into newborn mice produced developmental changes that could not be ascribed to nerve growth factor. These changes included precocious opening of the eyelids (7 days compared to the usual 14 days) and a similar early eruption of the incisors. Using these gross anatomical changes as an assay, Cohen (1962) proceeded to isolate the active factor — a polypeptide which he termed epidermal growth factor (EGF).
Ionospheric probing with an HF radar

The Jindalee over-the-horizon (OTH) radar is designed primarily for extended air defence surveillance of Australia's northern coastline. It achieves its long-range capability by employing ionospheric reflection. This use of the ionosphere allows the radar to have a powerful secondary role in remote sensing because information about the ionosphere can be made available as a byproduct of radar operations. Information about the ionosphere can be estimated for each radar resolution cell in range and azimuth. This information is updated each time the radar scans. The paper describes some of the remote-sensing capabilities of the Jindalee radar and presents some results concerning TIDs (travelling ionospheric disturbances), effects of the dawn terminator passage, geographic variations of ionisation density and meteor backscatter.
Corporate Governance Deviance

We develop the concept of corporate governance deviance and seek to understand why, when, and how a firm adopts governance practices that do not conform to the dominant governance logic. Drawing on institutional theory, coupled with both the entrepreneurship and corporate governance literature, we advance a middle-range theory of the antecedents of corporate governance deviance that considers both the institutional context and firm-level agency. Specifically, we highlight the centrality of a firm’s entrepreneurial identity as it interacts with the national governance logic to jointly create corporate governance discretion (i.e., the latitude of accessible governance practices) within the firm. We argue that as a firm’s governance discretion increases, it will be more likely to adopt overconforming or underconforming governance practices that deviate from established norms and practices. Moreover, we propose that adopting a deviant corporate governance practice is contingent on the governance regulatory en...
Social and economic impacts of climate

For centuries, thinkers have considered whether and how climatic conditions-such as temperature, rainfall, and violent storms-influence the nature of societies and the performance of economies. A multidisciplinary renaissance of quantitative empirical research is illuminating important linkages in the coupled climate-human system. We highlight key methodological innovations and results describing effects of climate on health, economics, conflict, migration, and demographics. Because of persistent "adaptation gaps," current climate conditions continue to play a substantial role in shaping modern society, and future climate changes will likely have additional impact. For example, we compute that temperature depresses current U.S. maize yields by ~48%, warming since 1980 elevated conflict risk in Africa by ~11%, and future warming may slow global economic growth rates by ~0.28 percentage points per year. In general, we estimate that the economic and social burden of current climates tends to be comparable in magnitude to the additional projected impact caused by future anthropogenic climate changes. Overall, findings from this literature point to climate as an important influence on the historical evolution of the global economy, they should inform how we respond to modern climatic conditions, and they can guide how we predict the consequences of future climate changes.
Consequences of the Clean Water Act and the Demand for Water Quality

Since the 1972 U.S. Clean Water Act, government and industry have invested over $1 trillion to abate water pollution, or $100 per person-year. Over half of U.S. stream and river miles, however, still violate pollution standards. We use the most comprehensive set of files ever compiled on water pollution and its determinants, including 50 million pollution readings from 240,000 monitoring sites and a network model of all U.S. rivers, to study water pollution's trends, causes, and welfare consequences. We have three main findings. First, water pollution concentrations have fallen substantially. Between 1972 and 2001, for example, the share of waters safe for fishing grew by 12 percentage points. Second, the Clean Water Act's grants to municipal wastewater treatment plants, which account for $650 billion in expenditure, caused some of these declines. Through these grants, it cost around $1.5 million (2014 dollars) to make one river-mile fishable for a year. We find little displacement of municipal expenditure due to a federal grant. Third, the grants' estimated effects on housing values are smaller than the grants' costs; we carefully discuss welfare implications.
Discourse on Leadership

In a wide-ranging and provocative new study, Bert A. Spector provides a critical analysis of past and present theories of leadership. Spector asserts that our perception of leadership influences who we vote for, who we hire and promote, and ultimately, who we choose to grant our authority to. Focusing on leadership in discourse, the book sets out to explore how the notion of leadership has been articulated, studied and debated by academics, but also by practitioners, journalists, and others who seek to influence the thoughts of others. Paying particular attention to the social, economic, political, intellectual and historical forces that have helped shape the discussion, Discourse on Leadership offers an insightful historiography of leadership as a concept and considers how our understanding of it continues to evolve.
TRIBOCORROSION AT MODULAR JUNCTIONS: HOW BIG A PROBLEM IS IT?

Corrosion at metal/metal modular interfaces in total hip arthroplasty was first described in the early 19909s, and the susceptibility of modular tapers to mechanically assisted crevice corrosion (MACC), a combination of fretting and crevice corrosion, was subsequently introduced. Since that time, there have been numerous reports of corrosion at this taper interface, documented primarily in retrieval studies or in rare cases of catastrophic failure. We have reported that fretting corrosion at the modular taper may produce soluble and particulate debris that can migrate locally or systemically, and more recently reported that this process can cause an adverse local tissue reaction. Based on the type of tissue reaction and the presence of elevated serum metal ion levels, this process appears quite similar to adverse local tissue reactions secondary to metal on metal bearing surfaces. While modularity in THR has demonstrable clinical benefits, modular junctions increase the risk of corrosion and the types of adverse soft tissue reactions seen in patients with accelerated metal release from metal-on-metal bearing THRs.
Serum total IgG and IgG4 levels in thyroid eye disease

Purpose To investigate the relationship between immunoglobulin G (IgG)4-related disease (IgG4-RD) and thyroid eye disease (TED) with respect to IgG levels. Patients and methods A retrospective review of total IgG, IgG subclass, and thyroid stimulating immunoglobulin (TSI) levels in 24 patients with TED. Results Five patients (20.8%) demonstrated serum IgG4 levels consistent with IgG4-RD without any additional systemic disease. Total IgG and IgG subclass levels were found to be an inadequate proxy for TSI elevation. Conclusion There may be a subtype of TED patients with elevated IgG4 in the absence of IgG4-RD systemic findings.
Minimizing the number of independent sets in triangle-free regular graphs

Abstract Recently, Davies, Jenssen, Perkins, and Roberts gave a very nice proof of the result (due, in various parts, to Kahn, Galvin–Tetali, and Zhao) that the independence polynomial of a d -regular graph is maximized by disjoint copies of K d , d . Their proof uses linear programming bounds on the distribution of a cleverly chosen random variable. In this paper, we use this method to give lower bounds on the independence polynomial of regular graphs. We also give a new bound on the number of independent sets in triangle-free cubic graphs.
Laplacian growth, sandpiles, and scaling limits

Laplacian growth is the study of interfaces that move in proportion to harmonic measure. Physically, it arises in fluid flow and electrical problems involving a moving boundary. We survey progress over the last decade on discrete models of (internal) Laplacian growth, including the abelian sandpile, internal DLA, rotor aggregation, and the scaling limits of these models on the lattice Z^d as the mesh size goes to zero. These models provide a window into the tools of discrete potential theory: harmonic functions, martingales, obstacle problems, quadrature domains, Green functions, smoothing. We also present one new result: rotor aggregation in Z^d has O(log r) fluctuations around a Euclidean ball, improving a previous power-law bound. We highlight several open questions, including whether these fluctuations are O(1).
Google's Multilingual Neural Machine Translation System: Enabling Zero-Shot Translation

We propose a simple solution to use a single Neural Machine Translation (NMT) model to translate between multiple languages. Our solution requires no changes to the model architecture from a standard NMT system but instead introduces an artificial token at the beginning of the input sentence to specify the required target language. Using a shared wordpiece vocabulary, our approach enables Multilingual NMT using a single model. On the WMT’14 benchmarks, a single multilingual model achieves comparable performance for English→French and surpasses state-of-the-art results for English→German. Similarly, a single multilingual model surpasses state-of-the-art results for French→English and German→English on WMT’14 and WMT’15 benchmarks, respectively. On production corpora, multilingual models of up to twelve language pairs allow for better translation of many individual pairs. Our models can also learn to perform implicit bridging between language pairs never seen explicitly during training, showing that transfer learning and zero-shot translation is possible for neural translation. Finally, we show analyses that hints at a universal interlingua representation in our models and show some interesting examples when mixing languages.
Learning-based view synthesis for light field cameras

With the introduction of consumer light field cameras, light field imaging has recently become widespread. However, there is an inherent trade-off between the angular and spatial resolution, and thus, these cameras often sparsely sample in either spatial or angular domain. In this paper, we use machine learning to mitigate this trade-off. Specifically, we propose a novel learning-based approach to synthesize new views from a sparse set of input views. We build upon existing view synthesis techniques and break down the process into disparity and color estimation components. We use two sequential convolutional neural networks to model these two components and train both networks simultaneously by minimizing the error between the synthesized and ground truth images. We show the performance of our approach using only four corner sub-aperture views from the light fields captured by the Lytro Illum camera. Experimental results show that our approach synthesizes high-quality images that are superior to the state-of-the-art techniques on a variety of challenging real-world scenes. We believe our method could potentially decrease the required angular resolution of consumer light field cameras, which allows their spatial resolution to increase.
Distribution of FDG-avid nodes in esophageal cancer: implications for radiotherapy target delineation

Clinical target volumes (CTV) for radiotherapy (RT) in esophageal cancer (EC) are based on standard expansions of primary tumor volume. Data is needed to define regions at highest risk for occult disease, based on histology and location of the primary tumor. We therefore reviewed PET scans in EC patients to characterize the location of FDG-avid lymph node metastases (LNM). We identified 473 EC patients with reviewable pre-treatment PET-CT scans. Tumors were classified by histology and location; 85% were distal or GE junction tumors and 71% were adenocarcinoma. FDG-avid LNM were classified using standard radiographic nodal atlases, and distances from primary tumor to paraesophageal LNM were also measured. The most common LNM in upper EC were supraclavicular, retrotracheal and paratracheal. The most common LNM in lower EC were paraesophageal and in the gastrohepatic space. Overall, 55% of paraesophageal LNM were adjacent to primary tumor. Of upper esophageal tumors with paraesophageal LNM, 87% were adjacent to the tumor and none were >6 cm from tumor. However, 57% of lower esophageal tumors with paraesophageal LNM had non-adjacent paraesophageal nodes, 24% of which were >8 cm from the tumor. A more data-driven and individualized approach to CTV delineation could improve the therapeutic ratio of RT in esophageal cancer. These results can guide CTV delineation by indicating the potential distribution of nodal involvement in esophageal cancer.
A Gaussian Mixture Model Smoother for Continuous Nonlinear Stochastic Dynamical Systems: Theory and Scheme

AbstractRetrospective inference through Bayesian smoothing is indispensable in geophysics, with crucial applications in ocean and numerical weather estimation, climate dynamics, and Earth system modeling. However, dealing with the high-dimensionality and nonlinearity of geophysical processes remains a major challenge in the development of Bayesian smoothers. Addressing this issue, a novel subspace smoothing methodology for high-dimensional stochastic fields governed by general nonlinear dynamics is obtained. Building on recent Bayesian filters and classic Kalman smoothers, the fundamental equations and forward–backward algorithms of new Gaussian Mixture Model (GMM) smoothers are derived, for both the full state space and dynamic subspace. For the latter, the stochastic Dynamically Orthogonal (DO) field equations and their time-evolving stochastic subspace are employed to predict the prior subspace probabilities. Bayesian inference, both forward and backward in time, is then analytically carried out in the...
An Improved Deterministic Rescaling for Linear Programming Algorithms

The perceptron algorithm for linear programming, arising from machine learning, has been around since the 1950s. While not a polynomial-time algorithm, it is useful in practice due to its simplicity and robustness. In 2004, Dunagan and Vempala showed that a randomized rescaling turns the perceptron method into a polynomial time algorithm, and later Pena and Soheili gave a deterministic rescaling. In this paper, we give a deterministic rescaling for the perceptron algorithm that improves upon the previous rescaling methods by making it possible to rescale much earlier. This results in a faster running time for the rescaled perceptron algorithm. We will also demonstrate that the same rescaling methods yield a polynomial time algorithm based on the multiplicative weights update method. This draws a connection to an area that has received a lot of recent attention in theoretical computer science.
Two-color multiphoton emission from nanotips

Two-color multiphoton emission from polycrystalline tungsten nanotips has been demonstrated using two-color laser fields. The two-color photoemission is assisted by a three-photon multicolor quantum channel, which leads to a twofold increase in quantum efficiency. Weak-field control of two-color multiphoton emission was achieved by changing the efficiency of the quantum channel with pulse delay. The result of this study complements two-color tunneling photoemission in strong fields, and has potential applications for nanowire-based photonic devices. Moreover, the demonstrated two-color multiphoton emission may be important for realizing ultrafast spin-polarized electron sources via optically injected spin current.
On Different "Middle Parts" of a Tree

We determine the maximum distance between any two of the center, centroid, and subtree core among trees with a given order. Corresponding results are obtained for trees with given maximum degree and also for trees with given diameter. The problem of the maximum distance between the centroid and the subtree core among trees with given order and diameter becomes difficult. It can be solved in terms of the problem of minimizing the number of root-containing subtrees in a rooted tree of given order and height. While the latter problem remains unsolved, we provide a partial characterization of the extremal structure.
A wireless sensing platform utilizing ambient RF energy

An ambient RF energy harvesting sensor node with onboard sensing and communication functionality was developed and tested. The minimal RF input power required for sensor node operation was -18 dBm (15.8 μW). Using a 6 dBi receive antenna, the most sensitive RF harvester was shown to operate at a distance of 10.4 km from a 1 MW UHF television broadcast transmitter, and over 200 m from a cellular base transceiver station. A complete ambient RF-powered prototype was constructed which measured temperature and light level and wirelessly transmitted these measurements.
Vertical channel devices enabled by through silicon via (TSV) technologies

Novel device structures with vertical channels gated by TSV's are demonstrated. The unique device structure is realized in a standard TSV process flow, without new material systems or processes. They can be used for both characterizing the TSV process as well as enable new functions. They can be easily integrated into product designs thus enabling field monitoring.
Unsupervised Visual-Linguistic Reference Resolution in Instructional Videos

We propose an unsupervised method for reference resolution in instructional videos, where the goal is to temporally link an entity (e.g., dressing) to the action (e.g., mix yogurt) that produced it. The key challenge is the inevitable visual-linguistic ambiguities arising from the changes in both visual appearance and referring expression of an entity in the video. This challenge is amplified by the fact that we aim to resolve references with no supervision. We address these challenges by learning a joint visual-linguistic model, where linguistic cues can help resolve visual ambiguities and vice versa. We verify our approach by learning our model unsupervisedly using more than two thousand unstructured cooking videos from YouTube, and show that our visual-linguistic model can substantially improve upon state-of-the-art linguistic only model on reference resolution in instructional videos.
Single-column model and large eddy simulation of the evening transition in the planetary boundary layer

In the present study, the well-known case of day 33 of the Wangara experiment is resimulated using the Weather Research and Forecasting (WRF) model in an idealized single-column mode to assess the performance of a frequently used planetary boundary layer (PBL) scheme, the Yonsei University PBL scheme. These results are compared with two large eddy simulations for the same case study imposing different surface fluxes: one using previous surface fluxes calculated for the Wangara experiment and a second one using output from the WRF model. Finally, an alternative set of eddy diffusivity equations was tested to represent the transition characteristics of a sunset period, which led to a gradual decrease of the eddy diffusivity, and replaces the instantaneous collapse of traditional diagnostics for eddy diffusivities. More appreciable changes were observed in air temperature and wind speed (up to 0.5 K, and 0.6 m s−1, respectively), whereas the changes in specific humidity were modest (up to 0.003 g kg−1). Although the representation of the convective decay in the standard parameterization did not show noticeable improvements in the simulation of state variables for the selected Wangara case study day, small changes in the eddy diffusivity over consecutive hours throughout the night can impact the simulation of distribution of trace gases in air quality models. So, this work points out the relevance of simulating the turbulent decay during sunset, which could help air quality forecast models to better represent the distribution of pollutants storage in the residual layer during the entire night.
Automated Phrase Mining from Massive Text Corpora

As one of the fundamental tasks in text analysis, phrase mining aims at extracting quality phrases from a text corpus and has various downstream applications including information extraction/retrieval, taxonomy construction, and topic modeling. Most existing methods rely on complex, trained linguistic analyzers, and thus likely have unsatisfactory performance on text corpora of new domains and genres without extra but expensive adaption. None of the state-of-the-art models, even data-driven models, is fully automated because they require human experts for designing rules or labeling phrases. In this paper, we propose a novel framework for automated phrase mining, $\mathsf{AutoPhrase}$ , which supports any language as long as a general knowledge base (e.g., Wikipedia) in that language is available, while benefiting from, but not requiring, a POS tagger. Compared to the state-of-the-art methods, $\mathsf{AutoPhrase}$ has shown significant improvements in both effectiveness and efficiency on five real-world datasets across different domains and languages. Besides, $\mathsf{AutoPhrase}$ can be extended to model single-word quality phrases.
Tropical compactification in log-regular varieties

In this article we define a natural tropicalization procedure for closed subsets of log-regular varieties in the case of constant coefficients and study its basic properties. This framework allows us to generalize some of Tevelev’s results on tropical compactification as well as Hacking’s result on the cohomology of the link of a tropical variety to log-regular varieties.
Inflation and string cosmology

I give a brief review of inflationary theory and of its recent progress related to string cosmology.
Asset Location, Timing Ability and the Cross‐Section of Commercial Real Estate Returns

This study examines the sensitivity of equity REIT returns to time‐varying MSA allocations of REIT property portfolios. Using a large sample of individual commercial property holdings, we find significant cross‐sectional and time variation in REIT geographic exposures and the ability of these exposures to explain the cross‐section of REIT returns. We further find evidence consistent with REIT managers being able, on average, to time allocation decisions ahead of MSA outperformance. This effect is most prevalent in non‐gateway markets, varies significantly across MSAs and over time, and is concentrated in financially flexible firms with a more diversified geographic portfolio.
OUTCOMES AND RADIOGRAPHIC FINDINGS OF ANATOMICAL PRESS-FIT RADIAL HEAD ARTHROPLASTY

Background Radial head arthroplasty (RHA) is a popular method of treatment for complex fractures of the radial head. The purpose of this study was to investigate patient outcomes and radiographic findings associated with a single anatomical monopolar press-fit radial head system commonly used for the treatment of radial head fractures. Methods A retrospective review of prospectively collected data was performed for a consecutive series of patients treated with RHA between November 2007 and April 2014. Patients with a minimum of 12-month follow-up were included. Most recent radiographs were evaluated for loosening, stress shielding, and instability. Post-operative motion and outcomes were reported at most-recent follow-up. Results At an average follow-up of 30 months, 7 of the 17 patients (41%) demonstrated radiographic loosening. Six of the 10 patients (60%) without loosening demonstrated stress shielding (average 6mm). Functional outcome scores included a mean ASES of 74, MEPS of 87, VAS Pain of 1, VAS Function of 8 and SANE of 79. Average flexion-extension arc was 13°–138°, and average pronation-supination was 77°–76° (Figure 1). Of the patients with radiographic loosening, 86% had undergone RHA with an associated ligamentous injury of the elbow. Satisfaction among patients was high, as no patient reported an unsatisfactory outcome. Conclusions The use of an anatomic, press-fit monopolar RHA in the management of acute complex radial head fractures has yielded excellent clinical outcomes despite high rates of radiographic loosening and stress shielding. Press-fit RHA in the setting of ligamentous injury warrants further investigation due to a high rate of implant loosening observed.
A SERENDIPITOUS, LONG-TERM INFILTRATION EXPERIMENT: WATER AND RADIONUCLIDE CIRCULATION BENEATH THE CAMBRIC TRENCH AT THE NEVADA TEST SITE.

Underground atomic weapons testing at the Nevada Test Site introduced numerous radionuclides that may be used to characterize subsurface hydrologic transport processes in arid climates. Beginning in 1975, groundwater adjacent to the CAMBRIC test, conducted beneath Frenchman Flat in 1965, was pumped steadily for 16 years to elicit experimental information on the migration of residual radioactivity through the saturated zone. Radionuclides in the pumping well effluent, including tritium, {sup 36}Cl and {sup 85}Kr, were extensively monitored prior to their discharge into an unlined ditch flowing toward a dry lake bed over a kilometer away. We have applied a large (6km x 6km x 1km) and highly resolved (4 m) variably saturated flow model to investigate infiltration into the 220-m vadose zone underlying the ditch as well as subsequent groundwater recharge and well recirculation processes. A Lagrangian particle-tracking model has been used to compute flow pathways and estimate radionuclide travel and residence times in various parts of the system based upon the flow model. Results are consistent with rising tritium levels observed in a monitoring well since 1991. They suggest that recirculation of the ditch effluent through the vadose zone, into groundwater, and back to the test cavity and pumping well are responsible for diluted, tritium-based groundwater age dates observed in 2000 at these locations, as well as for increased tailing effects observed in the pumping well elution curves. Altogether, the models and experimental observations provide an improved basis to understand both historical and future movements of test-related radionuclides in groundwater near CAMBRIC.
Hard X-ray-induced damage on carbon-binder matrix for in situ synchrotron transmission X-ray microscopy tomography of Li-ion batteries.

The electrode of Li-ion batteries is required to be chemically and mechanically stable in the electrolyte environment for in situ monitoring by transmission X-ray microscopy (TXM). Evidence has shown that continuous irradiation has an impact on the microstructure and the electrochemical performance of the electrode. To identify the root cause of the radiation damage, a wire-shaped electrode is soaked in an electrolyte in a quartz capillary and monitored using TXM under hard X-ray illumination. The results show that expansion of the carbon–binder matrix by the accumulated X-ray dose is the key factor of radiation damage. For in situ TXM tomography, intermittent X-ray exposure during image capturing can be used to avoid the morphology change caused by radiation damage on the carbon–binder matrix.
Lagrangian and Hamiltonian Taylor variational integrators

In this paper, we present a variational integrator that is based on an approximation of the Euler–Lagrange boundary-value problem via Taylor’s method. This can be viewed as a special case of the shooting-based variational integrator. The Taylor variational integrator exploits the structure of the Taylor method, which results in a shooting method that is one order higher compared to other shooting methods based on a one-step method of the same order. In addition, this method can generate quadrature nodal evaluations at the cost of a polynomial evaluation, which may increase its efficiency relative to other shooting-based variational integrators. A symmetric version of the method is proposed, and numerical experiments are conducted to exhibit the efficacy and efficiency of the method.
Efficient Simulation of Financial Stress Testing Scenarios with Suppes-Bayes Causal Networks

Abstract The most recent financial upheavals have cast doubt on the adequacy of some of the conventional quantitative risk management strategies, such as VaR (Value at Risk), in many common situations. Consequently, there has been an increasing need for verisimilar financial stress testings, namely simulating and analyzing financial portfolios in extreme, albeit rare scenarios. Unlike conventional risk management which exploits statistical correlations among financial instruments, here we focus our analysis on the notion of probabilistic causation, which is embodied by Suppes-Bayes Causal Networks (SBCNs), SBCNs are probabilistic graphical models that have many attractive features in terms of more accurate causal analysis for generating financial stress scenarios. In this paper, we present a novel approach for conducting stress testing of financial portfolios based on SBCNs in combination with classical machine learning classification tools. The resulting method is shown to be capable of correctly discovering the causal relationships among financial factors that affect the portfolios and thus, simulating stress testing scenarios with a higher accuracy and lower computational complexity than conventional Monte Carlo Simulations.
Assessing real-time Zika risk in the United States

Confirmed local transmission of Zika Virus (ZIKV) in Texas and Florida have heightened the need for early and accurate indicators of self-sustaining transmission in high risk areas across the southern United States. Given ZIKV’s low reporting rates and the geographic variability in suitable conditions, a cluster of reported cases may reflect diverse scenarios, ranging from independent introductions to a self-sustaining local epidemic. We present a quantitative framework for real-time ZIKV risk assessment that captures uncertainty in case reporting, importations, and vector-human transmission dynamics. We assessed county-level risk throughout Texas, as of summer 2016, and found that importation risk was concentrated in large metropolitan regions, while sustained ZIKV transmission risk is concentrated in the southeastern counties including the Houston metropolitan region and the Texas-Mexico border (where the sole autochthonous cases have occurred in 2016). We found that counties most likely to detect cases are not necessarily the most likely to experience epidemics, and used our framework to identify triggers to signal the start of an epidemic based on a policymakers propensity for risk. This framework can inform the strategic timing and spatial allocation of public health resources to combat ZIKV throughout the US, and highlights the need to develop methods to obtain reliable estimates of key epidemiological parameters.
Doctor-patient communication: a review and a rationale for using an assessment framework.

The purpose of this paper is to explore the extent to which improving doctor–patient communication (DPC) can address and alleviate many healthcare delivery inefficiencies.,The authors survey causes and costs of miscommunication including perceptual gaps between how physicians believe they perform their communicative duties vs how patients feel and highlight thresholds such as the Hospital Consumer Assessment of Healthcare Providers and Systems (HCAHPS) used by hospitals to identify health outcomes and improve DPC.,The authors find that DPC correlates with better and more accurate care as well as with more satisfied patients. The authors utilize an assessment framework, doctor–patient communication assessment (DPCA), empirically measuring the effectiveness of DPC. While patient care is sometimes viewed as purely technical, there is evidence that DPC strongly predicts clinical outcomes as well as patients’ overall ratings of hospitals.,More research is needed to extend our understanding of the impact of the DPC on the overall HCAHPS ratings of hospitals. The authors think that researchers should adopt a qualitative method (e.g. content analysis) for analyzing DPC discourse.,When a sufficient amount of DPCA training is initiated, a norming procedure could be developed and a database may be employed to demonstrate training program’s efficacy, a critical factor in establishing the credibility of the measurement program and nurturing support for its use.,The authors highlight clinical and operational issues as well as costs associated with miscommunication and the need to use metrics such as HCAHPS that allow consumers to see how hospitals differ on specific characteristics.
Noise and diffusion of a vibrated self-propelled granular particle

Granular materials are an important physical realization of active matter. In vibration-fluidized granular matter, both diffusion and self-propulsion derive from the same collisional forcing, unlike many other active systems where there is a clean separation between the origin of single-particle mobility and the coupling to noise. Here we present experimental studies of single-particle motion in a vibrated granular monolayer, along with theoretical analysis that compares grain motion at short and long time scales to the assumptions and predictions, respectively, of the active Brownian particle (ABP) model. Our results show that despite the unique relation between noise and propulsion, a variety of granular particles are correctly described by the ABP model. Additionally, our scheme of analysis for validating the inputs and outputs of the model can be applied to other granular and non-granular active systems.
A Combinatorial Proof of a Formula of Biane and Chapuy

Let $G$ be a simple strongly connected weighted directed graph. Let $\mathcal{G}$ denote the spanning tree graph of $G$. That is, the vertices of $\mathcal{G}$ consist of the directed rooted spanning trees on $G$, and the edges of $\mathcal{G}$ consist of pairs of trees $(t_i, t_j)$ such that $t_j$ can be obtained from $t_i$ by adding the edge from the root of $t_i$ to the root of $t_j$ and deleting the outgoing edge from $t_j$. A formula for the ratio of the sum of the weights of the directed rooted spanning trees on $\mathcal{G}$ to the sum of the weights of the directed rooted spanning trees on $G$ was recently given by Biane and Chapuy. Our main contribution is an alternative proof of this formula, which is both simple and combinatorial.
Urine Dipstick vs. Microscopic Urinalysis in the Evaluation of Abdominal Trauma

This study was designed to assess the accuracy of the urine dipstick and its ability to predict injury to the urinary tract when compared to routine urinalysis: 1,485 patients had dipstick and microscopic urinalysis performed as part of their evaluation for blunt and penetrating trauma. Dipstick analysis was recorded as either positive or negative. Microhematuria was defined as greater than 0-1 RBC/HPF on microscopic analysis. Blunt trauma accounted for 1,347 (91%) of the patients and penetrating injuries accounted for 138 cases (9%): 1,209 (81.4%) of the specimens were dipstick negative, and 276 (18.6%) were dipstick positive. False negative results, consisting of a negative dipstick reading and greater than 1 RBC/HPF on microscopic analysis occurred in 100 (6.9%) of the cases. False positive dipstick readings occurred in 64 (4.3%) of the patients. There were no cases of a missed injury in the group of 100 false negatives. Cost savings by conversion to the use of dipsticks would have saved our institution about $63,000 per year. It is concluded that the urinary dipstick is a safe, accurate, and reliable screening test for the presence or absence of hematuria in patients sustaining either blunt or penetrating abdominal trauma.
Exogenous Protein as the Cause of Nephrotic-Range Proteinuria

Hematuria and proteinuria developed in a young woman with waxing and waning symptoms suggestive of systemic lupus erythematosus. Quantitatively, the proteinuria was in the nephrotic range, but other manifestations of the nephrotic syndrome were absent. Serologic evaluation demonstrated normal results. The hematuria was subsequently found to be self-induced and related to foreign objects in the bladder. Urine protein electrophoresis confirmed severe proteinuria with a spike in the gamma region. Immunoelectrophoresis demonstrated that the proteinuria was not of human origin. Subsequent urinary protein values were normal. This case exhibits features compatible with Munchausen's syndrome and shows that severe proteinuria may be factitious.
Prostatic Hexosaminidase Activity in Patients With Benign Prostatic Hyperplasia and Prostatic Carcinoma

Hexosaminidase activity in prostatic tissue has been compared in 15 patients with benign prostatic hyperplasia and 15 patients with prostatic carcinoma. The ratio of enzymatic activity for the two substrates tested ( p -nitrophenyl-2-acetamido-2- deoxy-β-d-glucopyranoside and p -nitrophenyl-2-acetamido-2- deoxy-β-d-galactopyranoside) was not significantly different in the two groups of patients. The proportion of hexosaminidase represented by the B isozyme was not significantly different for the two groups of patients. Prostatic tissue hexosaminidase was greater ( p = 0.0141) in carcinomatous prostates than in hyperplastic prostates.
Tumor Biology in Explanation of the Failure of Screening for Cancer and in Determination of Future Strategies

Abstract Screening examinations for so-called "early cancer" are popular methods to decrease cancer mortality. This report reviews current concepts in tumor biology that explain why screening for cancer succeeds and why it fails. From this review, three biologic subgroups emerge for many cancers. In only one of these groups will screening methods be successful in decreasing death from cancer. Breast cancer and prostatic cancer are specifically considered to support this hypothesis. Implications for future investigations and the impact on public policy are discussed.
A Trial of Bacillus Calmette-Guérin Versus Adriamycin in Superficial Bladder Cancer: A South-West Oncology Group Study

One hundred and sixty-one evaluable patients with biopsy-confirmed transitional cell carcinoma of the bladder were studied in a cooperative protocol comparing intravesical BCG and adriamycin. Patients have been followed for 2-25 months (median 15.7 months) with cystoscopy at 3-month intervals, urinary cytology, and bladder biopsy. Sixteen of 88 patients (19%) who received BCG immunotherapy developed tumor recurrence compared with 45 recurrences (54%) in the 83 patients who received adriamycin chemotherapy (p less than 0.001, chi 2). Eighty-nine of the randomized patients had documented carcinoma in situ. The complete response rate in 41 patients with carcinoma in situ who received BCG was 85%, compared with a complete response rate of only 39% in 46 patients who received adriamycin (p less than 0.001, chi 2). These data suggest that BCG immunotherapy is superior to adriamycin chemotherapy in the prevention of recurrent superficial transitional cell carcinoma and the treatment of in situ carcinoma of the urinary bladder.
Modeling the synergistic elimination of bacteria by phage and the innate immune system

Phage therapy has been viewed as a potential treatment for bacterial infections for over a century. Yet, the year 2016 marks one of the first phase I/II human trials of a phage therapeutic - to treat burn wound patients in Europe. The slow progress in realizing clinical therapeutics is matched by a similar dearth in principled understanding of phage therapy. Theoretical models and in vitro experiments find that combining phage and bacteria often leads to coexistence of both phage and bacteria or phage elimination altogether. Both outcomes stand in contrast to the stated goals of phage therapy. A potential resolution to the gap between models, experiments, and therapeutic use of phage is the hypothesis that the combined effect of phage and host immune system can synergistically eliminate bacterial pathogens. Here, we propose a phage therapy model that considers the nonlinear dynamics arising from interactions between bacteria, phage and the host innate immune system. The model builds upon earlier efforts by incorporating a maximum capacity of the immune response and density-dependent immune evasion by bacteria. We analytically identify a synergistic regime in this model in which phage and the innate immune response jointly contribute to the elimination of the target bacteria. Crucially, we find that in this synergistic regime, neither phage alone nor the innate immune system alone can eliminate the bacteria. We confirm these findings using numerical simulations in biologically plausible scenarios. We utilize our numerical simulations to explore the synergistic effect and its significance for guiding the use of phage therapy in clinically relevant applications.
The Past, Present, and Future of Neurorehabilitation: From NUSTEP Through IV STEP and Beyond.

Purposes:To present the history and aims of the STEP conferences; describe the interdependence of prevention, prediction, plasticity, and participation; reflect on where we stand today regarding those 4 Ps; and discuss how future neurorehabilitation should look for individuals with movement disorder
A Complication of the Implantable Constant Infusion Chemotherapy Pump

The treatment of metastatic colorectal cancer to the liver has been a significant problem for clinicians in the past. Recent technical advances in infusion systems in the form of the infusaid pump has allowed delivery of chemotherapeutic agents to the liver with great reliability. As more chemotherapy pumps are implanted, undoubtedly, new and unusual complications will occur. This report centers on a patient who developed a disrupted catheter secondary to a high pressure side port injection. It includes a description of the complication, how it occurred, was recognized, and corrected. This report will, hopefully, save other clinicians from encountering similar complications in any of their patients.
Benchmarking Relatedness Inference Methods with Genome-Wide Data from Thousands of Relatives

Inferring relatedness from genomic data is an essential component of genetic association studies, population genetics, forensics, and genealogy. While numerous methods exist for inferring relatedness, thorough evaluation of these approaches in real data has been lacking. Here, we report an assessment of 12 state-of-the-art pairwise relatedness inference methods using a data set with 2485 individuals contained in several large pedigrees that span up to six generations. We find that all methods have high accuracy (92-99%) when detecting first- and second-degree relationships, but their accuracy dwindles to 76% of relative pairs. Overall, the most accurate methods are Estimation of Recent Shared Ancestry (ERSA) and approaches that compute total IBD sharing using the output from GERMLINE and Refined IBD to infer relatedness. Combining information from the most accurate methods provides little accuracy improvement, indicating that novel approaches, such as new methods that leverage relatedness signals from multiple samples, are needed to achieve a sizeable jump in performance.
Bootstrapping with Models: Confidence Intervals for Off-Policy Evaluation.

For an autonomous agent, executing a poor policy may be costly or even dangerous. For such agents, it is desirable to determine confidence interval lower bounds on the performance of any given policy without executing said policy. Current methods for exact high confidence off-policy evaluation that use importance sampling require a substantial amount of data to achieve a tight lower bound. Existing model-based methods only address the problem in discrete state spaces. Since exact bounds are intractable for many domains we trade off strict guarantees of safety for more data-efficient approximate bounds. In this context, we propose two bootstrapping off-policy evaluation methods which use learned MDP transition models in order to estimate lower confidence bounds on policy performance with limited data in both continuous and discrete state spaces. Since direct use of a model may introduce bias, we derive a theoretical upper bound on model bias for when the model transition function is estimated with i.i.d. trajectories. This bound broadens our understanding of the conditions under which model-based methods have high bias. Finally, we empirically evaluate our proposed methods and analyze the settings in which different bootstrapping off-policy confidence interval methods succeed and fail.
Contagious sets in dense graphs

We study the activation process in undirected graphs known as bootstrap percolation: a vertex is active either if it belongs to a set of initially activated vertices or if at some point it had at least r active neighbors, for a threshold r that is identical for all vertices. A contagious set is a vertex set whose activation results with the entire graph being active. Let m(G, r) be the size of a smallest contagious set in a graph G. We examine density conditions that ensure that a given n-vertex graph \(G=(V,E)\) has a small contagious set. With respect to the minimum degree, we prove that if G has minimum degree \(n{\slash }2\) then \(m(G,2)=2\). We also provide tight upper bounds on the number of rounds until all nodes are active.