gebhart/patrepeval huggingface dataset:
NOMAD: Deterministic collision-free channel access with channel reuse in wireless networks (2011)

The Neighborhood Ordering for Medium Access with Determinism (NOMAD) protocol is introduced. NOMAD defines collision-free transmission schedules dynamically and with no need for a predefined number of time slots per transmission frame by coordinating circular permutations of the identifier of nodes in the neighborhoods shared among nodes. NOMAD is shown to attain feasible transmission schedules within a short finite time and to provide channel access intervals of negligible variance. The performance of the NOMAD is compared with the performance of 802.11 DCF and the node activation multiple access (NAMA) protocol, which is representative of distributed transmission scheduling based on probabilistic elections. NOMAD is shown to attain higher throughput than 802.11 and NAMA in static and dynamic ad hoc networks, and to eliminate the large variances in channel access times present in contention-based schemes and prior transmission-scheduling schemes that do not use reservations.
Shortened β-cell lifespan leads to β-cell deficit in a rodent model of type 2 diabetes (2011)

Since the fundamental defect in both type 1 and type 2 diabetes is β-cell failure, there is increasing interest in the capacity, if any, for β-cell regeneration. Insights into typical β-cell age and lifespan during normal development and how these are influenced in diabetes is desirable to realistically establish the prospects for β-cell regeneration as means to reverse the deficit in β-cell mass in diabetes. We assessed the mean β-cell age and lifespan by the classical McKendrick-von Foester equation that describes the age-based heterogeneity of β-cells in terms of the time-varying β-cell formation and loss estimated by a β-cell turnover model. This modeling approach was applied to evaluate β-cell lifespan in a rodent model of type 2 diabetes in comparison with nondiabetic controls. When rats were 10 mo old, mean β-cell lifespan was 1 mo vs. 6 mo in rats with type 2 diabetes vs. controls. A shortened β-cell lifespan in a rat model of type 2 diabetes results in a decrease in mean β-cell age and thus contributes to decreased β-cell mass.
Impact of Ta Diffusion on the Perpendicular Magnetic Anisotropy of Ta/CoFeB/MgO (2013)

Effects of Ta diffusion on the perpendicular magnetic anisotropy (PMA) of Ta/Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> (12.5 Å)/MgO stacks were investigated. We found that Ta initially mixed with Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> and its diffusion became prominent above 300 °C. Initial diffusion of Ta into the Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> was not detrimental to the PMA, but a significant PMA reduction occurred when Ta migrated to the Co <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.6</sub> Fe <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> B <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0.2</sub> /MgO interface. This accounts for the fact that optimizing the PMA of Ta/CoFeB/MgO requires the tuning of both CoFeB thickness and annealing temperature.
High resolution imaging of intracellular dynamics in explanted retinas with dynamic full-field OCT (Conference Presentation) (2017)

Full-Field Optical Coherence Tomography (FF-OCT) reveals submicrometric morphological details in retinal explants without the use of contrast agents. Notably, in the nerve fiber and ganglion cell layers, FF-OCT images reveal nerve fibers bundles, single axons, capillaries and even some ganglion cell bodies. Dynamic FF-OCT (D-FF-OCT) takes advantage of the temporal evolution of the local FF-OCT signal to reveal a movement-dependent contrast inside tissues. Notably, the D-FF-OCT signal depends on cellular motility and membrane fluctuations. Compared to regular FF-OCT images, the signal from stationary structures such as nerve fibers is reduced, and contrast inside cells is enhanced, revealing many more cells, as well as the position of nuclei, and cell metabolism. We used a multimodal D-FF-OCT and fluorescence microscope to compare and identify the structures observed in both FF-OCT and D-FF-OCT. In the ganglion cell and inner nuclear layers in both macaque and mouse, two different cell sizes could be measured, which correlated well with ganglion and amacrine cell diameters found in the literature for these two species. We could also detect cell bodies of the photoreceptors in the outer nuclear layer. To our knowledge, this is the first time that an OCT technique can reveal these cell bodies. Finally, to investigate post-mortem tissue changes, time series were acquired over periods of 24 hours and cell contrast was plotted in time to monitor the decrease in intracellular activity over time. It is anticipated that dynamic FF-OCT may be used to non-invasively monitor viability and functional changes in the retina.
Design Considerations for ZnO Transistors Made Using Spatial ALD (2014)

We have used spatial atomic layer deposition (SALD) to fabricate metal oxide thin-film devices with unusually simple processes. Selective area deposition allows us to fabricate transistors and circuits additively and with digital design variations when used in combination with an inkjet-printed inhibitor. In a second approach, we use the conformal nature of SALD films to produce self-aligned sub-micron channel length vertical transistors that have large alignment tolerances and are suitable for high-performance thin-film electronics. We discuss device design considerations for both architectures.
Superradiance and Subradiance due to Quantum Interference of Entangled Free Electrons (2021)

When multiple quantum emitters radiate, their emission rate may be enhanced or suppressed due to collective interference in a process known as super- or subradiance. Such processes are well known to occur also in light emission from free electrons, known as coherent cathodoluminescence. Unlike atomic systems, free electrons have an unbounded energy spectrum, and, thus, all their emission mechanisms rely on electron recoil, in addition to the classical properties of the dielectric medium. To date, all experimental and theoretical studies of super- and subradiance from free electrons assumed only classical correlations between particles. However, dependence on quantum correlations, such as entanglement between free electrons, has not been studied. Recent advances in coherent shaping of free-electron wave functions motivate the investigation of such quantum regimes of super- and subradiance. In this Letter, we show how a pair of coincident path-entangled electrons can demonstrate either super- or subradiant light emission, depending on the two-particle wave function. By choosing different free-electron Bell states, the spectrum and emission pattern of the light can be reshaped, in a manner that cannot be accounted for by a classical mixed state. We show these results for light emission in any optical medium and discuss their generalization to many-body quantum states. Our findings suggest that light emission can be sensitive to the explicit quantum state of the emitting matter wave and possibly serve as a nondestructive measurement scheme for measuring the quantum state of many-body systems.
Cyclic Avian Mass Mortality in the Northeastern United States Is Associated with a Novel Orthomyxovirus (2014)

The emergence or reemergence of viral pathogens resulting in large-scale outbreaks of disease in humans and/or animals is one of the most important challenges facing biomedicine. For example, understanding how orthomyxoviruses such as novel influenza A virus reassortants and/or mutants emerge to cause epidemic or pandemic disease is at the forefront of current global health concerns. Here, we describe the emergence of a novel orthomyxovirus, Wellfleet Bay virus (WFBV), which has been associated with cyclic large-scale bird die-offs in the northeastern United States. This initial characterization study provides a foundation for further research into the evolution, epidemiology, and ecology of newly emerging orthomyxoviruses, such as WFBV, and their potential impacts on animal and/or human health.
Generalized Chirp-Like Sequences With Zero Correlation Zone (2010)

In this paper, a new construction of optimum sets of zero correlation zone (ZCZ) sequences, derived from generalized chirp-like (GCL) sequences, is presented. A special case with reduced alphabet size is also described. In a set of GCL-ZCZ sequences, the length of the zero correlation zone <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> has the maximum possible value <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">D</i> = <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">t</i> - 1 for a given sequence length <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> = <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">tm</i> and for a given number of sequences in the set <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</i> = <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">m</i> . Many values of <i xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">N</i> can be decomposed into multiple products of two positive integers, thus allowing for flexible tradeoff between the length of the ZCZ and the number of sequences in the set. As the set of GCL-ZCZ sequences is obtained by modulating a common ¿carrier¿ sequence with a set of orthogonal modulating sequences, there is a possibility for efficient implementation of the corresponding bank of matched filters.
Machine learning methods for microbiome studies (2020)

Researches on the microbiome have been actively conducted worldwide and the results have shown human gut bacterial environment significantly impacts on immune system, psychological conditions, cancers, obesity, and metabolic diseases. Thanks to the development of sequencing technology, microbiome studies with large number of samples are eligible on an acceptable cost nowadays. Large samples allow analysis of more sophisticated modeling using machine learning approaches to study relationships between microbiome and various traits. This article provides an overview of machine learning methods for non-data scientists interested in the association analysis of microbiomes and host phenotypes. Once genomic feature of microbiome is determined, various analysis methods can be used to explore the relationship between microbiome and host phenotypes that include penalized regression, support vector machine (SVM), random forest, and artificial neural network (ANN). Deep neural network methods are also touched. Analysis procedure from environment setup to extract analysis results are presented with Python programming language.
Distributed hierarchical reinforcement learning in multi-agent adversarial environments (2022)

We develop a hierarchical approach for controlling a team of aircraft in multi-agent adversarial environments. Each individual aircraft is equipped with a high-level agent that is solely responsible for target assignment decisions, and a low-level agent that generates actions based only on the selected target. We use distributed deep reinforcement learning to train the high-level agents, and neuroevolution to train the low-level agents. This approach leverages centralized training for decentralized execution to enable individual autonomy when communication is limited. Simulation results confirm the superiority of our proposed approach as compared to non-hierarchical multi-agent reinforcement learning methods.
Orbitrap Mass Spectrometry: A Proposal for Routine Analysis of Nonvolatile Components of Petroleum (2011)

High-resolution mass spectrometry can provide a detailed fingerprint of the composition of the nonvolatile fraction of petroleum. That analysis is typically performed using Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometry, which offers greater mass resolution than any other mass analyzer. While high resolution is desirable for complex mixtures, such as petroleum, the high costs associated with FT-ICR limit its use to a small number of research laboratories, limiting the impact of the measurement relative to more accessible techniques. Here, we explore whether there is a role for other high-resolution mass analyzers to complement FT-ICR. One such high-resolution mass analyzer is the LTQ Orbitrap XL, which presents significantly lower costs relative to typical FT-ICR instruments. The Orbitrap mass analyzer provides mass resolution inferior to the modern FT-ICR instrument but still sufficient to assign molecular formulas to individual components present in mixtures, especially those components present in relatively high abundance. Indeed, the resolution of the LTQ Orbitrap XL is comparable to that obtained by FT-ICR instruments 1 decade ago, at which time FT-ICR was being used successfully to fingerprint petroleum. Here, we demonstrate successful application of the Orbitrap to resolve and identify >1000 of the more abundant molecular formulas in the negative ion electrospray ionization mass spectrum of a petroleum sample. These results are compared to the 9.4 T FT-ICR analysis of the same sample (published previously; Pomerantz, A. E.; Ventura, G. T.; McKenna, A. M.; Cañas, J.; Auman, J.; Koerner, K.; Curry, D.; Nelson, R. K.; Reddy, C. M.; Rodgers, R. P.; Marshall, A. G.; Peters, K. E.; Mullins, O. C.Combining biomarker and bulk compositional gradient analysis to assess reservoir connectivity. Org. Geochem. 2010, 41, 812–821), and in this analysis, both the compositional fingerprints and conclusions derived from those fingerprints are essentially the same for the FT-ICR and Orbitrap data. Setting up and operating a LTQ Orbitrap XL mass spectrometer presents significantly lower initial and continuing costs compared to setting up and operating a 9.4 T FT-ICR, and this difference may make the Orbitrap accessible to laboratories for which FT-ICR is cost-prohibitive. Although several valuable high-resolution mass spectrometric analyses require the extremely high resolution of FT-ICR, we propose Orbitrap mass spectrometry as a method for routine analysis of the composition of the more abundant species in the nonvolatile and polar fraction of petroleum. Extending the realm of high-resolution mass spectrometry from a limited research environment to routine analysis would increase the utility of the technique and the impact of fundamental research regarding mass spectrometry of petroleum.
Adaptive Parameter Estimation for Aerial Manipulation (2020)

This paper proposes a model reference adaptive controller for aerial robots equipped with manipulators for grasping and transporting objects of unknown mass. Through a Lyapunov argument, this estimation and control algorithm is shown to be asymptotically stable when tracking a desired reference trajectory. The adaptive controller is then demonstrated on a quadrotor with a changing total mass, showing that it can track a reference trajectory with sufficient accuracy to pick up a payload and maintain flight stability, despite the sudden change in vehicle parameters induced by the payload. This new adaptive controller is slower to respond to changes in vehicle mass than control strategies that use more conventional mass estimation methods, but it is subject to less noise since it does not make use of accelerometer data, resulting in a smoother control trajectory.
Delay Modulation in Separately Driven Delay Cells Utilized for the Generation of High-Performance Multiphase Signals Using ROs (2021)

This brief presents a general technique for achieving the highest possible RO oscillation frequency accompanied by lower phase noise in an enhanced circuit design utilizing novel delay cells. The circuit architecture has the delay cells’ inputs separated by an optimized skew offset. Skew-offset optimization is attained by integrating a pre-charge/discharge auxiliary feed-forward loop into the separately driven delay cells. This technique reduces the transition time when <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">Supply</i> and GND are simultaneously connected/disconnected to the delay cell’s output node. When these delay cells are connected in loops to form a Ring Oscillator, they provide high performance, even/odd multi-phase signals. The proposed methodology is validated in commercial 65nm and 180nm CMOS technologies. The post-layout simulations show that the proposed designs improve the performance by modulating the delay cell output node’s charging and discharging. The operating frequency of the proposed design, e.g., for odd stage 5/7 and even stage 4/8/16 stage, is almost 50%/40%, (80%/30%/20%) higher than that of the MSSRO (Multi-Loop Skew based Single-ended Ring Oscillator) with the same number of stages. Additionally, the designs proposed for the targeted phase noise and center frequency consume around 8–20% (odd stages)/ (6–28%) (Even stages) lesser power, a lower supply sensitivity up to 9%, and lower PVT variability up to 6% compared to its equivalent stages MSSRO (3-stages single-ended RO) counterparts in 180 nm CMOS Technology.
TREATMENT OF EARLY AND INTERMEDIATE STAGES OF COLORECTAL CANCER WITH EGF‐RECEPTOR RELATED PROTEIN (ERRP). (2007)

Selective anticancer therapies suppress the activation of individual members of the EGFR family. Since most solid tumors express several members of EGFRs, this may not be sufficient to suppress tumor formation. EGF‐Receptor Related Protein (ERRP), a pan‐erbB inhibitor, targets multiple members of EGFRs. In the present study, we studied the effect of recombinant ERRP on the regression of carcinogen‐induced ACF in CF1 mice, representing early stages of colon cancer. As a model for intermediate stages, we used C57Bl/6JMin/+ (Min) mice that carry mutations in the APC gene. ERRP treatment began only after establishment of ACF in CF1 mice or adenoma formation in Min mice. Mice were injected daily with 50 ug ERRP or vehicle (controls) for 10 days. This led to a 40–50% reduction of ACF (p&lt;0.05) and their size (P&lt;0.05). In Min mice, we found a drastic reduction of tumor number and size. The changes in both models were associated with a significant inhibition (50–60%) of proliferation and stimulation (60–70%) of apoptosis in the intestinal mucosa, accompanied by a marked reduction in activation and expression of EGFR, HER‐2 and HER‐3 as well as activation of IGF‐1R and inhibition of NF‐kappa‐B. In contrast, the activity of intestinal alkaline phosphatase, a marker of differentiation, was greatly elevated following ERRP treatment. Taken together, the results indicate that ERRP is effective in inducing regression of existing early and intermediate stages of colorectal cancer. This could partly be attributed to inhibition of EGFRs signaling and induction of differentiation of intestinal mucosa. We suggest that ERRP could be an effective agent for colorectal cancer.
The emerging era of cell engineering: Harnessing the modularity of cells to program complex biological function (2022)

A new era of biological engineering is emerging in which living cells are used as building blocks to address therapeutic challenges. These efforts are distinct from traditional molecular engineering-their focus is not on optimizing individual genes and proteins as therapeutics, but rather on using molecular components as modules to reprogram how cells make decisions and communicate to achieve higher-order physiological functions in vivo. This cell-centric approach is enabled by a growing tool kit of components that can synthetically control core cell-level functional outputs, such as where in the body a cell should go, what other cells it should interact with, and what messages it should transmit or receive. The power of cell engineering has been clinically validated by the development of immune cells designed to kill cancer. This same tool kit for rewiring cell connectivity is beginning to be used to engineer cell therapies for a host of other diseases and to program the self-organization of tissues and organs. By forcing the conceptual distillation of complex biological functions into a finite set of instructions that operate at the cell level, these efforts also shed light on the fundamental hierarchical logic that links molecular components to higher-order physiological function.
Comparison by mass spectrometry of ring cleavage in barbituric acid and 5‐fluorobarbituric acid derivatives (1992)

Abstract The mass spectrometric behaviour of barbituric acid and 1,3‐dimethylbarbituric acid was compared with that of the corresponding 5,5‐difluoro derivatives and of some 5‐fluoro‐5‐alkyl derivatives in order to study the influence of fluorine in the fragmentation processes. This investigation, performed using both electron impact ionization and positive‐ and negative‐ion fast atom bombardment, evidences well the role of fluorine in barbiturate ring bond cleavages.
Handheld Projectors for Mixing Physical and Digital Textures (2006)

Handheld projectors offer a new type of display modality, not tied to a physical screen or to a fixed projection area, yet providing a larger display than is available from a handheld device with fixed screen. This paper begins with a review of our prototype handheld projector, and describes our work on interaction using a cursor that can be tracked across the projection. The most immediate use for such a device is to support existing applications like web-browsing. We show examples of this type of application. But there is a broader question too - does a handheld projector support new types of application that are not available with a physical screen or a fixed projection? We describe two applications that illustrate how the combination of handheld projection plus interaction supports ways to interact with the physical world that are much more natural than via conventional displays.