gebhart/patrepeval huggingface dataset:
Clos‐Network Switches (2006)

This chapter contains sections titled: Routing Property of Clos Network Switches Looping Algorithm m-Matching Algorithm Euler Partition Algorithm Karol's Algorithm Frame-Based Matching Algorithm for Clos Network (f-MAC) Concurrent Matching Algorithm for Clos Network (c-MAC) Dual-Level Matching Algorithm for Clos Network (d-MAC) The ATLANTA Switch Concurrent Round-Robin Dispatching (CRRD) Scheme The Path Switch
Single-molecule imaging in solution with total internal reflection excitation (2000)

Summary form only given.The detection of individual single-chromophore molecules in aqueous solution, first demonstrated with picoliter-sized sample volumes, and soon after with femtoliter-sized volumes, has become routinely achievable. More recently, the imaging of individual single-chromophore molecules in very thin layers of aqueous solution, using epifluorescence and total internal reflection (TIR) microscopies has been reported.
Advanced Computer Vision(Module 5F16) (2006)

Summary Intro: Probabilistic models Two different approaches for learning Generative/discriminative models, discriminative functions Advanced segmentation system: GrabCut
ChemInform Abstract: Structure‐Activity Relationships for the Antileishmanial and Antitrypanosomal Activities of 1′‐Substituted 9‐Anilinoacridines. (1997)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Towards faster data access: Seek operations in MEMS-based storage devices (2006)

Even in the most advanced hard-disk drives (HDDs), data access is a slow process because of the relatively large mechanical structures, the one-dimensional actuation capability of the head, and the latency due to rotating disks. It is expected that MEMS-based storage devices with two-dimensional actuation capability could significantly improve the speed of data access. In this paper we demonstrate this experimentally with a MEMS-based probe-storage prototype using a micro-scanner that serves as the positioner for the storage medium. First the theoretically minimum achievable seek times are derived for the micro-scanner by approximating its dynamics with a damped harmonic oscillator model. Then the similarity of the time-optimal solution with that of the better studied double integral system is exploited to employ a proximate-time-optimal controller for the experimental studies. The experimental results demonstrate seek times of approximately 1.6 ms for seek operations of 50 μm.
Turbo-encoder design for symbol-interleaved parallel concatenated trellis-coded modulation (2001)

This paper addresses turbo-encoder design for coding with high spectral efficiency using parallel concatenated trellis-coded modulation and symbol interleaving. The turbo-encoder design involves the constituent encoder design and the interleaver design. The constituent encoders are optimized for symbol-wise effective free distance, and each has an infinite symbol-wise impulse response. We identify the canonical structures for the constituent encoder search space. In many cases of practical interest, the optimal structure for these constituent encoders connects the memory elements in a single row. This single row generally applies to turbo code constituent encoders for parallel concatenation and is not restricted to symbol interleaving. To lower the error floor, a new semi-random interleaver design criteria and a construction method extends the spread-interleaver concept introduced by Divsalar and Pollara (1995). Simulation results show that the proposed system employing symbol interleaving can converge at a lower signal-to-noise ratio than previously reported systems. We report simulation results between 0.5 and 0.6 db from constrained capacity for rates of 2 and 4 bits/s/Hz.
Clear Cell Endocrine Pancreatic Tumor Mimicking Renal Cell Carcinoma (2001)

The dominantly inherited von Hippel–Lindau disease is characterized by clear cell neoplasms in various organs including the kidney and pancreas. Determination of primary versus metastatic lesion in this setting can be a diagnostic dilemma. The authors present five cases of clear cell endocrine pancreatic tumor (EPT) closely mimicking renal cell carcinomas in five patients with a family history or histologic evidence of von Hippel–Lindau disease. In fact, two of these tumors were confused with metastatic renal cell carcinoma by fine-needle aspiration. All five tumors had a component of clear cells arranged in nests, cords, and tubules with central hemorrhage separated by thin-wall vessels resembling renal cell carcinoma. However, these tumors also exhibited cords and festoons and a gyriform pattern suggestive of an endocrine neoplasm, and expressed chromogranin and synaptophysin. Vascular invasion was identified in four tumors, one of which metastasized. The concurrent primary renal cell carcinomas and the multicentric microcystic adenomas found in three patients did not show reactivity for the neuroendocrine markers. Focal clear cell change was noted in only one of 29 endocrine pancreatic tumors arising in patients without von Hippel–Lindau disease. Eleven metastatic renal cell carcinomas in the pancreas did not show immunoreactivity with the endocrine markers. Clear cell EPTs closely mimicking renal cell carcinoma are distinctive neoplasms of von Hippel–Lindau disease. In contrast to clear cell EPT, metastatic renal cell carcinoma does not express neuroendocrine markers and lacks neurosecretory granules by electron microscopy. Von Hippel–Lindau disease should be strongly suspected in patients with renal cell carcinoma, clear cell EPT, and multifocal microcystic serous adenomas.
Estimation of the Rate of Penetration While Horizontally Drilling Carbonate Formation Using Random Forest (2021)

Abstract Predicting the rate of penetration (ROP) is challenging especially during horizontal drilling. This is because there are many factors affecting ROP. Machine learning techniques are very promising in identifying the structural relationships existing between the inputs and target variables; these techniques were recently successfully applied to estimate the ROP in different wellbore shapes and through various formation lithologies. This study is aimed to introduce a random forest (RF) regression model for ROP prediction based on many factors such as the drilling mechanical parameters (torque, pipe speed, and weight on bit), hole cleaning parameters (the drilling fluid flowrate and pump pressure), and formation properties (formation bulk density and formation resistivity). In addition to its superiority in providing accurate results, RF has the advantage of providing interpretable rules. These rules help in understanding the relationships between the regressors and the target variable. Actual field measurements collected during horizontally drilling carbonate formation were used for training and testing the RF model. Unseen data collected from another well were used for validating the optimized model. Using the K-fold validation method, the proposed RF model has proven its superior performance when compared to artificial neural networks and support vector regression models. An illustrative example on a sample of real drilling data is presented to explain how the RF regression model is applied to the drilling data. In addition, developing interpretable regression rules through merging RF results is explained. These rules can guide drilling practitioners in accomplishing drilling projects at minimum time and cost.
A Three Degree of Freedom Pseudo-Rigid-Body Model for the Design of a Fully Compliant Bistable Micromechanism (2002)

A three degree-of-freedom (3DOF) Pseudo-Rigid-Body Model (PRBM) has been developed and used in the design of a new class of Self-Retracting Fully compliant Bistable Micromechanism, or SRFBM. The SRFBM provides small-displacement linear travel bistability and is suitable for low-power microswitching applications. The design process involved a combination of single and multiple degree-of-freedom PRBM and finite element models to quickly proceed from a rigid-body concept to fully compliant fabrication-ready geometry. The 3DOF model presented here was developed to more accurately model the behavior of the tensural pivots—a new class of compliant segment used to avoid combined compressive loading of flexible segments. Four SRFBM designs were fabricated and tested for bistability, on-chip actuation, critical force, and fatigue tests. These tests validate the models used in the design process and demonstrate the functionality and reliability of the SRFBM.
Synthesis and Thermodynamic Properties of Poly(cyclohexylethylene-b-dimethylsiloxane-b-cyclohexylethylene) (2007)

Poly(styrene-b-dimethylsiloxane-b-styrene) (PS−PDMS−PS) triblock copolymers were prepared by anionic polymerization and subsequently hydrogenated using a platinum/rhenium catalyst supported on ultrawide pore silica (Pt/Re−SiO2), yielding PCHE−PDMS−PCHE, where PCHE refers to poly(cyclohexylethylene). The hydrogenation reaction resulted in polymer with negligible chain degradation as confirmed by 1H NMR and size exclusion chromatography (SEC). Small-angle X-ray scattering (SAXS) and transmission electron microscopy (TEM) experiments revealed a lamellar morphology for all specimens. Thermodynamic properties were inferred from the order−disorder transition temperatures as determined by SAXS and dynamical mechanical spectroscopy (DMS). The resulting segment−segment interaction parameter, χ(T), is assessed in the context of current published approaches to treating the thermodynamics of nonpolar polyolefins, particularly block copolymers.
Cerebrospinal fluid–based kinetic biomarkers of axonal transport in monitoring neurodegeneration (2012)

Progress in neurodegenerative disease research is hampered by the lack of biomarkers of neuronal dysfunction. We here identified a class of cerebrospinal fluid-based (CSF-based) kinetic biomarkers that reflect altered neuronal transport of protein cargo, a common feature of neurodegeneration. After a pulse administration of heavy water (2H2O), distinct, newly synthesized 2H-labeled neuronal proteins were transported to nerve terminals and secreted, and then appeared in CSF. In 3 mouse models of neurodegeneration, distinct 2H-cargo proteins displayed delayed appearance and disappearance kinetics in the CSF, suggestive of aberrant transport kinetics. Microtubule-modulating pharmacotherapy normalized CSF-based kinetics of affected 2H-cargo proteins and ameliorated neurodegenerative symptoms in mice. After 2H2O labeling, similar neuronal transport deficits were observed in CSF of patients with Parkinson's disease (PD) compared with non-PD control subjects, which indicates that these biomarkers are translatable and relevant to human disease. Measurement of transport kinetics may provide a sensitive method to monitor progression of neurodegeneration and treatment effects.
Electrogenicity of hepatocellular fatty acid uptake. (1998)

Sensitivity of cellular fatty acids uptake to the membrane potential difference is still a matter of controversy. For direct evaluation of potential sensitivity the effect of changing membrane potential on uptake of a fluorescent long chain fatty acid derivative, 12-NBD-stearate, in isolated rat hepatocytes, was examined. Changes in membrane potential were achieved by patch clamp procedures. Fatty acid influx was simultaneously determined by recording of cell fluorescence. Hyperpolarization from -30 to -70 mV accelerated fatty acid influx whereas depolarization to +50 mV reduced uptake. After obtaining equilibrium hyperpolarization increased cell fluorescence, whereas depolarization pushed NBD-stearate out of cells. Potential sensitivity of uptake was dependent on the fatty acid concentrations in the medium with most prominent effects at low unbound concentrations. These data show that, at low fatty acid concentrations, uptake is, in part, driven by an intracellular negative electric membrane potential.
A nevv method for detecting late potentials using multichannel ECGs (2003)

We developed a procedure that is able to detect, quantify and localize late potentials that will also be applicable to patients with abnormally wide QRS complexes.
Analysis of the flicker level generated by the grid-connection of a fleet of electric vehicles (2016)

Optimised strategies regarding the coordinated grid connection of a fleet of electric vehicles often consider the simultaneous connection of a large number of these vehicles. This may induce voltage fluctuations of significant amplitude and provoke objectionable light intensity variations when applied to lighting equipment, which is defined as flicker. Hence, it is important to study under which conditions flicker may arise in order to define optimised grid connection strategies which prevent this phenomenon from occuring. However, although the grid impact of electric vehicle fleets is an active area of research, very few papers have considered the flicker level which the grid connection of electric vehicles may generate. Hence, this paper addresses the flicker level induced by the step-by-step grid connection of a fleet of electric vehicles connected to the distribution network. Flicker level will be studied under different conditions in terms of grid short-circuit level, grid impedance angle and power consumption profiles of the electric vehicle fleet.
Learning to Drive Off Road on Smooth Terrain in Unstructured Environments Using an On-Board Camera and Sparse Aerial Images (2020)

We present a method for learning to drive on smooth terrain while simultaneously avoiding collisions in challenging off-road and unstructured outdoor environments using only visual inputs. Our approach applies a hybrid model-based and model-free reinforcement learning method that is entirely self-supervised in labeling terrain roughness and collisions using on-board sensors. Notably, we provide both first-person and overhead aerial image inputs to our model. We nd that the fusion of these complementary inputs improves planning foresight and makes the model robust to visual obstructions. Our results show the ability to generalize to environments with plentiful vegetation, various types of rock, and sandy trails. During evaluation, our policy attained 90% smooth terrain traversal and reduced the proportion of rough terrain driven over by 6.1 times compared to a model using only first-person imagery. Video and project details can be found at www.cim.mcgill.ca/mrl/offroad_driving/.
Overview on the history of organofluorine chemistry from the viewpoint of material industry (2009)

Fluorine (from "le fluor", meaning "to flow") is a second row element of Group 17 in the periodic table. When bound to carbon it forms the strongest bond in organic chemistry to give organofluorine compounds. The scientific field treating them, organofluorine chemistry, started before elemental fluorine itself was isolated. Applying the fruits in academia, industrial organofluorine chemistry has developed over 80 years via dramatic changes during World War II. Nowadays, it provides various materials essential for our society. Recently, it utilizes elemental fluorine itself as a reagent for the introduction of fluorine atoms to organic molecules in leading-edge industries. This paper overviews the historical development of organofluorine chemistry especially from the viewpoint of material industry.
Intramolecular Interactions and Regulation of Cofactor Binding by the Four Repressive Elements in the Caspase Recruitment Domain-containing Protein 11 (CARD11) Inhibitory Domain (2016)

The CARD11 signaling scaffold transmits signaling between antigen receptors on B and T lymphocytes and the transcription factor NF-κB during the adaptive immune response. CARD11 activity is controlled by an inhibitory domain (ID), which participates in intramolecular interactions and prevents cofactor binding prior to receptor triggering. Oncogenic CARD11 mutations associated with the activated B cell-like subtype of diffuse large B cell lymphoma somehow perturb ID-mediated autoinhibition to confer CARD11 with the dysregulated spontaneous signaling to NF-κB that is required for the proliferation and survival of the lymphoma. Here, we investigate how the four repressive elements (REs) we have discovered in the CARD11 ID function to inhibit CARD11 activity with cooperativity and redundancy. We find that each RE contributes to the maintenance of the closed inactive state of CARD11 that predominates in the absence of receptor engagement. Each RE also contributes to the prevention of Bcl10 binding in the basal unstimulated state. RE1, RE2, and RE3 participate in intramolecular interactions with other CARD11 domains and share domain targets for binding. Remarkably, diffuse large B cell lymphoma-associated gain-of-function mutations in the caspase recruitment domain, LATCH, or coiled coil can perturb intramolecular interactions mediated by multiple REs, suggesting how single amino acid oncogenic CARD11 mutations can perturb or bypass the action of redundant inhibitory REs to achieve the level of hyperactive CARD11 signaling required to support lymphoma growth.
Author response: Pharmacological hallmarks of allostery at the M4 muscarinic receptor elucidated through structure and dynamics (2023)

Structural biology studies reveal the importance of protein dynamics on understanding molecular mechanisms underlying allosteric modulation of G protein-coupled receptors (GPCR) that offer insights into future GPCR research and drug discovery.
Performance of solid oxide fuel cells approaching the two-dimensional limit (2014)

We model electrochemical kinetics and physical conduction mechanisms for carrier transport in electrolyte membranes to determine the limits of dimensionality reduction (down to 1 nm) on maximum power output of solid oxide fuel cells with symmetric Pt electrodes. Using Y-doped ZrO2, we find a minimum thickness of ∼6 nm to realize near ideal chemical potential in such fuel cells, which is limited by electronic breakdown when approaching the dielectric breakdown strength. For larger electrolyte thicknesses, the greatest source of electronic leakage influencing power loss is from Ohmic transport of minority carriers and emission of trapped carriers. For porous metallic electrodes, an ideal microstructure with the particle size comparable to particle spacing dimensions is found to accurately model experimental results. The role of electronic trap states in the electrolyte band gap on power density characteristics is highlighted.
Geo-Supervised Visual Depth Prediction (2019)

We propose using global orientation from inertial measurements, and the bias it induces on the shape of objects populating the scene, to inform visual three-dimensional reconstruction. We test the effect of using the resulting prior in-depth prediction from a single image, where the normal vectors to surfaces of objects of certain classes tend to align with gravity or be orthogonal to it. Adding such a prior to baseline methods for monocular depth prediction yields improvements beyond the state-of-the-art and illustrates the power of gravity as a supervisory signal.
Model-Based Analysis of Electrode Placement and Pulse Amplitude for Hippocampal Stimulation (2018)

Beyond deepening understanding of the hippocampal tissue system, establishment of this model provides a method to evaluate candidate stimulating devices and protocols.
Distributed Lossy Averaging (2009)

An information theoretic formulation of the distributed averaging problem previously studied in computer science and control is presented. We assume a network with m nodes each observing a WGN source. The nodes communicate and perform local processing with the goal of computing the average of the sources to within a prescribed mean squared error distortion. The network rate distortion function R^*(D) for a 2-node network with correlated Gaussian sources is established. A general cutset lower bound on R^*(D) is established and shown to be achievable to within a factor of 2 via a centralized protocol over a star network. A lower bound on the network rate distortion function for distributed weighted-sum protocols, which is larger in order than the cutset bound by a factor of log m is established. An upper bound on the network rate distortion function for gossip-base weighted-sum protocols, which is only log log m larger in order than the lower bound for a complete graph network, is established. The results suggest that using distributed protocols results in a factor of log m increase in order relative to centralized protocols.
Abstract A36: Organoid models for deciphering roles of the evolving landscape of epigenetic heterogeneity during aging in cancer development (2020)

Abstract Background: Tumor initiation and development occur not necessarily by genetic changes alone, but in the context of the epigenome and cell microenvironment. Growing evidence indicate that cancer risk factors, such as aging and inflammation, may primarily modulate the epigenome, causing predisposition to cancer development by driver mutations. Thus, there is a need to study and model epigenetic changes preceding and associating with cancer development. We have developed ex vivo models for investigating the evolution and roles of DNA methylation changes during normal cell divisions and how these epigenetic changes play critical roles in early stages of tumor development. Results: We showed that spontaneous epigenetic changes, specifically promoter-DNA hypermethylation, have a very important role in tumor initiation by oncogenic driver mutations. We addressed the precursor role of aging-like spontaneous promoter-DNA hypermethylation in initiating tumorigenesis. Using mouse colon-derived organoids, we show promoter hypermethylation spontaneously arises in cells mimicking the human “aging-like” phenotype. The silenced genes activate the Wnt pathway, causing a stemlike state and differentiation defects. These changes render aged organoids profoundly more sensitive than young ones to transformation by BrafV600E producing the typical human proximal BRAFV600E-driven colon adenocarcinomas characterized by extensive, abnormal gene promoter CGI methylation or the methylator phenotype (CIMP). Conversely, CRISPR-mediated simultaneous inactivation of a panel of the silenced genes markedly sensitized to BrafV600E-induced transformation. We showed that “spontaneous” promoter hypermethylation, arising in an “aging-like” scenario, sufficiently affects genes with roles in negative regulation of Wnt pathway. Inactivation of these genes leads to increased stem cell state and defects in differentiation. Conclusion: Our studies tightly link aging-like epigenetic abnormalities to intestinal cell fate changes and predisposition to oncogene-driven colon tumorigenesis. The organoid-based model opens up an opportunity to study mechanisms underlying epigenetic heterogeneity arising during normal cellular processes and their role in cancer predisposition. Citation Format: Yong Tao, Byunghak Kang, Daniel Petkovich, Steve Baylin, Hariharan Easwaran. Organoid models for deciphering roles of the evolving landscape of epigenetic heterogeneity during aging in cancer development [abstract]. In: Proceedings of the AACR Special Conference on the Evolving Landscape of Cancer Modeling; 2020 Mar 2-5; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2020;80(11 Suppl):Abstract nr A36.