gebhart/patrepeval huggingface dataset:
Protection reconfiguration for reusable software (2002)

Secure distributed applications often include code to authenticate users, verify access rights, and establish secure communication channels between software components (e.g., clients and servers). This code is often specific to the application and to the context in which the application is used. Embedding protection definitions in the application code makes it difficult to reuse because different applications often have very different protection constraints. We argue that protection definitions should be specified separately from application code in order to facilitate protection reconfiguration and software reuse. This separation may be achieved by specifying protection definitions in a Protection Interface Definition Language, and is implemented by proxies installed between software components that are executing in different protection contexts (e.g., between client and server). Mechanisms for creation and dynamic installation of protection proxies have been implemented in a distributed shared memory system, and the viability of our solution is demonstrated by a simple name server, which is currently being reused in three different protection contexts.
Using Geometric Constraints for Camera Calibration and Positioning and 3D Scene Modelling (2004)

International audience
Robust synchronization of the cell cycle and the circadian clock through bidirectional coupling (2019)

The cell cycle and the circadian clock represent major cellular rhythms, which appear to be coupled. Thus the circadian factor BMAL1 controls the level of cell cycle proteins such as Cyclin E and WEE1, the latter of which inhibits the kinase CDK1 that governs the G2/M transition. In reverse the cell cycle impinges on the circadian clock through direct control by CDK1 of REV-ERBα, which negatively regulates BMAL1. These observations provide evidence for bidirectional coupling of the cell cycle and the circadian clock. By merging detailed models for the two networks in mammalian cells, we previously showed that unidirectional coupling to the circadian clock can entrain the cell cycle to 24 or 48 h, depending on the cell cycle autonomous period, while complex oscillations occur when entrainment fails. Here we show that the reverse unidirectional coupling via phosphorylation of REV-ERBα or via mitotic inhibition of transcription, both controlled by CDK1, can elicit entrainment of the circadian clock by the cell cycle. We then determine the effect of bidirectional coupling of the cell cycle and circadian clock as a function of their relative coupling strengths. In contrast to unidirectional coupling, bidirectional coupling markedly reduces the likelihood of complex oscillations. While the two rhythms oscillate independently as long as both couplings are weak, one rhythm entrains the other if one of the couplings dominates. If the couplings in both directions become stronger and of comparable magnitude, the two rhythms synchronize, generally at an intermediate period within the range defined by the two autonomous periods prior to coupling. More surprisingly, synchronization may also occur at a period slightly below or above this range, while in some conditions the synchronization period can even be much longer. Two or even three modes of synchronization may sometimes coexist, yielding examples of birhythmicity or trirhythmicity. Because synchronization readily occurs in the form of simple periodic oscillations over a wide range of coupling strengths and in the presence of multiple connections between the two oscillatory networks, the results indicate that bidirectional coupling favours the robust synchronization of the cell cycle and the circadian clock.
Abstract A70: Studying the signaling pathways of tumorigenic epithelial fallopian tube subpopulations during early tumorigenesis (2020)

Abstract Survival rates for high-grade serous ovarian carcinoma (HGSOC) patients have not substantially improved over the past decades, mainly because the disease is only detected at the metastatic stage. The findings of early premalignant lesions in the fallopian tube, but not in the ovary, suggested that HGSOCs may originate from the fallopian tube epithelium (FTE) and metastasize to the ovary. Studying the mechanisms of HGSOC genesis from the correct cell of origin is critical to the early detection of the disease. Our main goal is to determine how genetic and molecular alterations contribute to the early events of HGSOC genesis from FTE. Deletion of PTEN alone in FTE is sufficient to lead to tumor formation and peritoneal dissemination, suggesting that loss of PTEN may play a pivotal role in the early events of the tumorigenic cascade. Herein we show that loss of PTEN in the FTE upregulates markers of tumor-initiating cells (TIC) such as WNT4, LGR5, ALDH1, c-Kit, CD44, and Dll4. We also discovered that the TIC markers are confined in a specific population of cells with increased diameter that we call TICHigh as compared to a smaller population that we call TICLow. In fact, when these two populations are separated by flow cytometry-based sorting, the TICHigh retains all the TIC markers. In addition, using a limiting dilution assay, we found that the TICHigh subpopulation forms tumor at a faster rate in vivo and colonize more the ovary ex vivo. In addition, TICHigh forms bigger spheroids and are more resistant to chemotherapeutic agents, suggesting that more targeted therapy may be developed for these stem-like, tumorigenic subpopulations. We also show that loss of PAX2 is mediating the TICHigh phenotype and that activation of AKT is not sufficient to induce the TIC phenotype whereas p70S6K activation is required. These findings suggest that therapies to re-express PAX2 may prevent development of HGSOC. Together, these findings provide a novel model to study the mechanism of fallopian tube tumor initiation and invasion to the ovary mediated by loss of PTEN, which may help to define early events of human ovarian carcinogenesis. Citation Format: Angela Russo, Matthew Dean, Dan Lantvit, Joanna E. Burdette. Studying the signaling pathways of tumorigenic epithelial fallopian tube subpopulations during early tumorigenesis [abstract]. In: Proceedings of the AACR Special Conference on Advances in Ovarian Cancer Research; 2019 Sep 13-16, 2019; Atlanta, GA. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(13_Suppl):Abstract nr A70.
New Methodologies for Pharmacological Treatment Trials for Alcohol Dependence (1996)

As the number of pharmacological agents for the treatment of alcoholism continues to proliferate, there is an increasing need to design studies that accurately measure the efficacy of these agents. Key study design issues include selecting subjects, calculating patient retention, determining medication compliance, maintaining adequate sample size to ensure that a clinically meaningful therapeutic effect will not be missed, and measuring the study outcome, including the amount of alcohol consumed and levels of craving. Because there is evidence that self-report of alcohol consumption and medication compliance can be unreliable in subjects, biological methods have been used. One type of direct measurement, carbohydrate-deficient transferrin levels, has been found to be a reasonably sensitive indicator of alcohol consumption that may provide meaningful outcome information. The ingestion of riboflavin with medication and its urinary measurement is an accepted method of compliance detection. Improved study design will lead to continued advances in pharmacotherapy for the treatment of patients with alcoholism.
Using the Segmented Iterative Learning Control Method to Generate Volumetric Error-Compensated Part Programs for Three-Axis CNC Milling Machine Tools (2018)

This study proposes using the iterative learning control method to adjust the volumetric error-compensated tool path, where the working volume motion accuracy of three-axis computerized numerical control (CNC) milling machine tools is increased by segmented modification of the part program. As the three-axis CNC milling machine tools generally have volumetric error of working volume, this study refers to the measured and established table of volumetric errors and uses the method of the modifying part program for volumetric error compensation of machine tools. This study proposes using part-program single-block positioning segmented for volumetric error compensation, as the generated compensated part program with multiple compensated blocks can effectively compensate the volumetric error of working volume in the tool moving process. In terms of the compensated tool path computing method, this study uses the iterative learning control (ILC) method and refers to compensated tool path and volumetric errors along the compensated tool path for iterative computation. Finally, a part program with multiple blocks is modified by the converged optimal compensated tool path, in order that the modified part program has higher-precision volumetric error compensation effect. The simulation result shows that the rate of improvement of error of the volumetric error compensation method proposed in this study is 70%. The result of cutting tests shows that the average rate of improvement of the straightness error of the test workpiece is 60%, while the average rate of improvement of height error is 80%. Therefore, the results of simulation and cutting tests can prove the feasibility of using the ILC method for segmented modification of the volumetric error-compensated part programs proposed in this study.
3D human motion capture from monocular image sequences (2015)

This paper tackles the problem of estimating non-rigid human 3D shape and motion from image sequences taken by uncalibrated cameras. Similar to other state-of-the-art solutions we factorize 2D observations in camera parameters, base poses and mixing coefficients. Existing methods require sufficient camera motion during the sequence to achieve a correct 3D reconstruction. To obtain convincing 3D reconstructions from arbitrary camera motion, our method is based on a-priorly trained base poses. We show that strong periodic assumptions on the coefficients can be used to define an efficient and accurate algorithm for estimating periodic motion such as walking patterns. For the extension to non-periodic motion we propose our novel regularization term based on temporal bone length constancy. In contrast to other works, the proposed method does not use a predefined skeleton or anthropometric constraints and can handle arbitrary camera motion. Multiple experiments based on a 3D error metric demonstrate the stability of the proposed method. Compared to other state-of-the-art methods our algorithm shows a significant improvement.
Dynamics of Attached Cavities on Bodies of Revolution (1992)

Attached cavitation was generated on two axisymmetric bodies, a Schiebe body and a modified ellipsoidal body (the I. T. T. C. body), both with a 50.8 mm diameter. Tests were conducted for a range of cavitation numbers and for Reynolds numbers in the range of Re = 4.4 × 105 to 4.8 × 105. Partially stable cavities were observed. The steady and dynamic volume fluctuations of the cavities were recorded through measurements of the local fluid impedance near the cavitating surface suing a series of flush mounted electrodes. These data were combined with photographic observations. On the Schiebe body, the cavitation was observed to form a series of incipient spot cavities which developed into a single cavity as the cavitation number was lowered. The incipient cavities were observed to fluctuate at distinct frequencies. Cavities on the I. T. T. C. started as a single patch on the upper surface of the body which grew to envelope the entire circumference of the body as the cavitation number was lowered. These cavities also fluctuated at distinct frequencies associated with oscillations of the cavity closure region. The cavities fluctuated with Strouhal numbers (based on the mean cavity thickness) in the range of St = 0.002 to 0.02, which are approximately one tenth the value of Strouhal numbers associated with Ka´rma´n vortex shedding. The fluctuation of these stabilized partial cavities may be related to periodic break off and filling in the cavity closure region and to periodic entrainment of the cavity vapor. Cavities on both headforms exhibited surface striations in the streamwise direction near the point of cavity formation, and a frothy mixture of vapor and liquid was detected under the turbulent cavity surface. As the cavities became fully developed, the signal generated by the frothy mixture increased in magnitude with frequencies in the range of 0 to 50 Hz.
Steerable Importance Sampling (2007)

We present an algorithm for efficient stratified importance sampling of environment maps that generates samples in the positive hemisphere defined by local orientation of arbitrary surfaces while accounting for cosine weighting. The importance function is dynamically adjusted according to the surface normal using steerable basis functions. The algorithm is easy to implement and requires no user-defined parameters. As a preprocessing step, we approximate the incident illumination from an environment map as a continuous piecewise linear function on P <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and represent this as a triangulated height field. The product of this approximation and a dynamically orientable steering function, viz. the cosine lobe, serves as an importance sampling function. Our method allows the importance function to be sampled with an asymptotic cost of O(logn) per sample where n is the number of triangles. The most novel aspect of the algorithm is its ability to dynamically compute normalization factors which are integrals of the illumination over the positive hemispheres defined by the local surface normals during shading. The key to this feature is that the weight variation of each triangle due to the clamped cosine steering function can be well approximated by a small number of spherical harmonic coefficients which can be accumulated over any collection of triangles, in any orientation, without introducing higher-order terms. Consequently, the weighted integral of the entire steerable piecewise-linear approximation is no more costly to compute than that of a single triangle, which makes re-weighting and re-normalizing with respect to any surface orientation a trivial constant-time operation. The choice of spherical harmonics as the set of basis functions for our steerable importance function allows for easy rotation between coordinate systems. Another novel element of our algorithm is an analytic parametrization for generating stratified samples with linearly-varying density over a triangular support.
Figure S6 from Nicotinamide Phosphoribosyltransferase Acts as a Metabolic Gate for Mobilization of Myeloid-Derived Suppressor Cells (2023)

&lt;p&gt;G-CSF and M-CSF control NAMPT-dependent regulation of CXCR4&lt;/p&gt;
SIMULATION OF ALUMINUM FLAME STRUCTURE RELATING TO THE IMPORTANCE OF HETEROGENEOUS SURFACE REACTIONS (2016)

Surface reactions occur during the combustion of aluminum particles in various environments. In solid-propellant/rocket-motor conditions (at agglomerated particle sizes greater than 100 μm and pressure greater than 6.0 MPa), the gas-phase flame dominates the heat feedback to the molten aluminum particle and consumption of the aluminum particle. Combustion regimes where the gas-phase flame dominates have been the focus of much experimental and computational research. Recent experimental and computational work has shown that at low pressures and small particle sizes the kinetic rate of reaction is slower compared to the diffusion rate of the species moving the gaseous flame closer to the surface. This paper reports the results of aluminum particle combustion simulations over a wide range of oxidizer concentrations, pressures, and particle diameters depicting the transition regime from diffusion reactions to kinetic reactions. Calculated burn times are compared with experimental data. Computed flame structures under the various experimental test conditions are compared. Calculated species profiles are used to determine which species are present at the particle surface in the different combustion regimes. Calculations were performed to compare when the simulations transition to kinetic-controlled combustion in oxidizing environments made up of CO2, H2O, and O2. The calculations focus on the transition regime and do not consider the actual surface reactions of the aluminum particle.
Genome Sequence of Madurella mycetomatis mm55, Isolated from a Human Mycetoma Case in Sudan (2016)

We present the first genome sequence for a strain of the main mycetoma causative agent, Madurella mycetomatis This 36.7-Mb genome sequence will offer new insights into the pathogenesis of mycetoma, and it will contribute to the development of better therapies for this neglected tropical disease.
Post-mortem on a deep learning contest: a Simpson's paradox and the\n complementary roles of scale metrics versus shape metrics (2021)

To understand better good generalization performance in state-of-the-art\nneural network (NN) models, and in particular the success of the ALPHAHAT\nmetric based on Heavy-Tailed Self-Regularization (HT-SR) theory, we analyze of\na corpus of models that was made publicly-available for a contest to predict\nthe generalization accuracy of NNs. These models include a wide range of\nqualities and were trained with a range of architectures and regularization\nhyperparameters. We break ALPHAHAT into its two subcomponent metrics: a\nscale-based metric; and a shape-based metric. We identify what amounts to a\nSimpson's paradox: where "scale" metrics (from traditional statistical learning\ntheory) perform well in aggregate, but can perform poorly on subpartitions of\nthe data of a given depth, when regularization hyperparameters are varied; and\nwhere "shape" metrics (from HT-SR theory) perform well on each subpartition of\nthe data, when hyperparameters are varied for models of a given depth, but can\nperform poorly overall when models with varying depths are aggregated. Our\nresults highlight the subtlety of comparing models when both architectures and\nhyperparameters are varied; the complementary role of implicit scale versus\nimplicit shape parameters in understanding NN model quality; and the need to go\nbeyond one-size-fits-all metrics based on upper bounds from generalization\ntheory to describe the performance of NN models. Our results also clarify\nfurther why the ALPHAHAT metric from HT-SR theory works so well at predicting\ngeneralization across a broad range of CV and NLP models.\n
On expander codes (2001)

Sipser and Spielman (see ibid., vol.42, p.1717-22, Nov. 1996) have introduced a constructive family of asymptotically good linear error-correcting codes-expander codes-together with a simple parallel algorithm that will always remove a constant fraction of errors. We introduce a variation on their decoding algorithm that, with no extra cost in complexity, provably corrects up to 12 times more errors.
The conical Radon transform with vertices on triple lines (2020)

We study the inversion of the conical Radon which integrates a function in three-dimensional space from integrals over circular cones. The conical Radon recently got significant attention due to its relevance in various imaging applications such as Compton camera imaging and single scattering optical tomography. The unrestricted conical Radon transform is over-determined because the manifold of all cones depends on six variables: the center position, the axis orientation and the opening angle of the cone. In this work, we consider a particular restricted transform using triple line sensors where integrals over a three-dimensional set of cones are collected, determined by a one-dimensional vertex set, a one-dimensional set of central axes, and the one-dimensional set of opening angle. As the main result in this paper, we derive an analytic inversion formula for the restricted conical Radon transform. Along that way we define a certain ray transform adapted to the triple line sensor for which we establish an analytic inversion formula.
Summary of Inventory Pilot Project March 1993 - December 1994 (1994)

The Lean Aircraft Initiative began in the summer of 1992 as a “quick look” into the feasibility of applying manufacturing principles that had been pioneered in the automobile industry, most notably the Toyota Production System, to the U.S. defense aircraft industry. Once it was established that “lean principles” (the term coined to describe the new paradigm in automobile manufacturing) were indeed applicable to aircraft manufacturing as well, the Initiative was broadened to include other segments of the defense aerospace industry. These consisted of electronics/avionics, engines, electro-mechanical systems, missiles, and space systems manufacturers. In early 1993, a formal framework was established in which 21 defense firms and the Air Force formed a consortium to support and participate in the Initiative at M.I.T.
Correlation between structural disorder and electric properties in YBa2Cu3O7−δ (YBCO) (2006)

The degradation of the surface resistance Rs of YBCO material by ion milling is usually supposed to be linked to oxygen loss and crystallographic defects. To study this effect, the structural and physical analysis of the milled YBCO thin film has been carried out using Ion Beam Analyses and SQUID measurements. The cationic composition and the oxygen quantity measured in the disordered layer on the top of the film are the same on milled and reference samples. An increase of the bulk defect concentration, especially in the oxygen sublattice, is observed in the layer underlying the disordered layer. From SQUID measurements, the milled sample shows a degradation of susceptibility vs temperature X(T) compared to the reference sample. This observation is in a good agreement with the structural analysis and the Rs measurements. After an oxygen annealing at 450°C on the milled samples, the cationic disorder decreased and the bulk defect concentration has not been affected. The X(T) characteristic has improved for the milled film showing its correlation with the evolution of the disordered layer. However the Rs value of the annealed material is not restored.
Application of real-time rt-pcr utilising lux (light upon extension) fluorogenic primer for the rapid detection of avian influenza viruses (2006)

A real-time RT-PCR assay utilising light upon extension fluorogenic primer (LUX RT-PCR) was developed for the rapid and efficient detection of avian influenza viruses (AIV). The assay detected each of the AIV isolates tested (16/16) and gave negative results with heterologous pathogens (17/17). The detection limit of the assay proved to be 10(-0.5) EID50/0.2 ml and 10(1.5) EID50/0.2 ml in allantoic fluid of virus-infected embryonated chicken eggs and in spiked chicken faeces samples, respectively. Based on its specificity, sensitivity and relative simplicity, the LUX RT-PCR assay provides a novel, rapid and cost-effective diagnostic tool for avian influenza surveillance and monitoring programs.