gebhart/patrepeval huggingface dataset:
Trends in spectral analysis: higher order and cyclic statistics (1995)

Signal processing problems dealing with linear non-Gaussian signals, nonlinearities, and nonstationarities, cannot be addressed completely using time-invariant second-order statistical descriptors. Traditional correlation and spectral analysis are currently generalized to higher-order moments, cumulants, and polyspectra. At the same time there is an effort to cope with structured nonstationarities and in particular with cyclostationary processes which are signals exhibiting periodicity in their statistical behavior. A critical overview of higher-order and cyclic spectral analysis is attempted herein with emphasis on statistical signal processing aspects. Major advances and limitations are described along with some directions for future research.
Single photon nonlinear optics on photonic crystal chips (2009)

The promise of quantum information processing is driving developments in several different physical implementations. Photons are attractive as carriers of quantum information because they can travel long distances without losing their information through interactions with their environment. However, their passive nature can be a problem in applications such as the construction of logic gates, where it is necessary for two or more photons to interact. This interaction requires a nonlinear optical medium. Particularly strong nonlinearities are achieved when photons drive an emitter near its resonance frequency, and this nonlinearity is even greater if the photon is confined near the emitter in an optical cavity. We work with single semiconductor quantum dots (QDs) coupled to photonic crystal nanocavities. Recently, we showed that such a system enables an optical nonlinearity1 at the single-photon level: the cavity transmission spectrum changes dramatically when the power nears one intracavity photon number 〈ncav〉 per cavity lifetime (see Figure 1). The transmission spectrum obtained in the cross-polarized configuration shown in Figure 1(a) changes as plotted in Figure 1(b) when 〈ncav〉 increases from nearly zero to 〈ncav〉 ∼ 5. This nonlinearity relies on saturation of the QD, which occurs when the photon flux reaches roughly one photon per emitter lifetime. This single-photon-level nonlinearity has many promising applications. One application of particular interest in quantum information processing concerns the realization of large phase shifts on a signal beam conditioned on the intensity of a control beam. Using a homodyne setup, we measured the phase of the transmission through the cavity near the QD resonance frequency.2 As the probe power increases to 〈ncav〉 ∼ 3 and the QD saturates, we found that the phase of the transmitted beam changes by up to 0.24π . In applications such as quantum Figure 1. Resonant probing of the quantum dot (QD)-cavity system. (a) The cavity is probed by a vertically (V) polarized laser beam. The transmission of the cavity is detected in the orthogonal polarization (H) in order to reduce direct scattering from the incident beam. We model the quantum dot as an excited (e) and ground state (g) which is coupled to the cavity mode by a rate g. (b) The transmission spectrum shows the vacuum Rabi splitting due to the strongly coupled QD. The splitting disappears as the QD is saturated at an intracavity photon number 〈ncav〉 near unity. (c) The phase of the signal beam changes by up to 0.16π when the control beam intensity is raised to an incident power of 1μW, corresponding to 〈ncav〉 ≈ 1.
Field Ionization (FI) (2016)

This document contains recommendations for terminology in mass spectrometry. Development of standard terms dates back to 1974 when the IUPAC Commission on Analytical Nomenclature issued recommendations on mass spectrometry terms and definitions. In 1978, the IUPAC Commission on Molecular Structure and Spectroscopy updated and extended the recommendations and made further recommendations regarding symbols, acronyms, and abbreviations. The IUPAC Physical Chemistry Division Commission on Molecular Structure and Spectroscopy’s Subcommittee on Mass Spectroscopy revised the recommended terms in 1991 and appended terms relating to vacuum technology. Some additional terms related to tandem mass spectrometry were added in 1993 and accelerator mass spectrometry in 1994. Owing to the rapid expansion of the field in the intervening years, particularly in mass spectrometry of biomolecules, a further revision of the recommendations has become necessary. This document contains a comprehensive revision of mass spectrometry terminology that represents the current consensus of the mass spectrometry community.
A calcium-binding, asparagine-linked oligosaccharide is involved in skeleton formation in the sea urchin embryo. (1989)

We have previously identified a 130-kD cell surface protein that is involved in calcium uptake and skeleton formation by gastrula stage embryos of the sea urchin Strongylocentrotus purpuratus (Carson et al., 1985. Cell. 41:639-648). A monoclonal antibody designated mAb 1223 specifically recognizes the 130-kD protein and inhibits Ca+2 uptake and growth of the CaCO3 spicules produced by embryonic primary mesenchyme cells cultured in vitro. In this report, we demonstrate that the epitope recognized by mAb 1223 is located on an anionic, asparagine-linked oligosaccharide chain on the 130-kD protein. Combined enzymatic and chemical treatments indicate that the 1223 oligosaccharide contains fucose and sialic acid that is likely to be O-acetylated. Moreover, we show that the oligosaccharide chain containing the 1223 epitope specifically binds divalent cations, including Ca+2. We propose that one function of this negatively charged oligosaccharide moiety on the surfaces of primary mesenchyme cells is to facilitate binding and sequestration of Ca+2 ions from the blastocoelic fluid before internalization and subsequent deposition into the growing CaCO3 skeleton.
Metabolic heat and CO2 production rates during germination of melon (Cucumis melo L.) seeds measured by microcalorimetry (2001)

Abstract Metabolic heat and CO 2 production rates were measured by microcalorimetry during germination of two melon ( Cucumis melo L.) accessions, Noy Yizre’el (a cold-sensitive cultivar) and Persia 202 (a cold-tolerant breeding line), differing in their ability to germinate at low temperature (14°C). In seeds that were imbibed at either 14 or 25°C, both heat production rates ( φ ) and CO 2 evolution rates ( R CO 2 ) WERE HIGHER IN PERSIA 202 COMPARED TO NOY YIZRE’EL. AT 14°C, Φ AND R CO 2 of intact Noy Yizre’el seeds remained close to zero and germination was inhibited, but metabolic activity increased with time in decoated seeds (testa removed) and most embryos germinated. The presence of the testa had less effect on metabolic activity or germination of Persia 202 seeds at 14°C. The ratio of φ / R CO 2 (calorespirometric ratio) is an indication of the substrate being utilized for respiration, with lower values (∼455 kJ mol –1 ) associated with carbohydrate substrates and higher values (∼800 kJ mol –1 ) associated with lipid substrates. Removal of the testae of Noy Yizre’el seeds increased φ / R CO 2 at 14°C, suggesting that improved oxygen supply to the embryo promotes a shift from carbohydrate to lipid respiratory substrates associated with germination. Consistent with this interpretation, when the hilum apertures of the seed coats were sealed with silicone, φ , R CO 2 and φ / R CO 2 of Noy Yizre’el seeds remained low and germination was inhibited at 25°C, while in Persia 202 seeds the same treatment had relatively little effect on φ and R CO 2 , φ / R CO 2 approached the value expected for lipid respiratory substrates (700 kJ mol –1 ), and germination occurred. This confirms earlier anatomical work indicating that the testae of Persia 202 seeds were more porous than were those of Noy Yizre’el seeds, contributing to the greater tolerance of Persia 202 seeds to low temperatures. Abscisic acid (ABA) was also inhibitory to melon seed germination; imbibition of seeds at 25°C in 250 μM ABA decreased φ and R CO 2 , and φ / R CO 2 remained lower than in control seeds in both genotypes. This effect of ABA on metabolic activity could be a cause or consequence of inhibition of germination.
Zero Solid Invasion Water-Based Drilling Fluid (2018)

Abstract Reducing the filtrate volume and eliminating the solid invasion is very important and critical in drilling tight reservoir. This will eliminate water blocking which is the common problem in drilling tight gas formation. The objectives of this study are to evaluate the effect of using sodium silicate, assess the changes of the rheological properties of water-based drilling fluid, determine filtrate volume and filter cake thickness, and optimize the concentration of sodium silicate to be used. The obtained results showed that there was no effect of adding sodium silicate to the drilling fluid on density and pH. At room temperature, the optimum concentration of sodium silicate was 0.075 wt.% wt. which no change was observed in the yield point plastic viscosity ratio and at the same time, the plastic viscosity, yield point, and gel strength were enhanced. At higher temperature 120 and 170℉, the optimum concentration of sodium silicate was 0.075 wt.% which enhanced the rheological properties of the drilling fluid. Sodium silicate worked as a catalyst and as a result, it enhanced barite solubility at 200℉. The cumulative filtrate volume was decreased by 53% when using 0.075 wt.% of sodium silicate and the filter cake thickness was decreased by 65%. The retained permeability was 100% and the CT number before filtration and after removal was very closed, confirming no solid invasion was observed in the core.
B11-P-10Effects of secondaryγ' precipitates during creep in a single crystal Ni-based superalloy (2015)

Ni-based single crystal (SC) superalloys possess comprehensive properties like fracture strength, good fatigue and environmental resistance, in particular, the excellent resistance to creep deformation. Rafting was considered to be the main creep mechanism for the high-temperature and low-stress creep in Ni-based SC superalloys [ 1 ]. For most of the SC superalloys after full heat treatment, the ordered intermetallic γ' precipitate was formed and embedded in the disorder matrix in SC superalloys, referred to as primary γ' precipitates. However, small-sized-ordered γ' precipitate, referred to as secondary γ' precipitate or tertiary γ' precipitate, nucleated in the γ matrix, during higher undercooling [ 2 ] or creep deformation. The secondary γ' precipitate as well as the primary γ' precipitate was reported to contribute to improve the creep resistence at elevated temperature, which can effectively hinder the motion of dislocations in γ matrix channel and improve the creep resistence [ 3 ].
<title>New class of optoelectronic oscillators (OEO) for microwave signal generation and processing</title> (1996)

A new class of oscillators based on photonic devices is presented. These opto-electronic oscillators (OEO's) generate microwave oscillation by converting continuous energy from a light source using a feedback circuit which includes a delay element, an electro-optic switch, and a photodetector. Different configurations of OEO's are presented, each of which may be applied to a particular application requiring ultra-high performance, or low cost and small size.
The role of defects in resistively switching chalcogenides (2010)

Abstract This overview describes the present understanding of resistive switching phenomena encountered in chalcogenide-based cells which may be utilized in energy-efficient non-volatile memory devices and in array-based logic applications. We introduce the basic operation principle of the phase change mechanism, the thermochemical mechanism, and the valence change mechanism and we discuss the crucial role of structural defects in the switching processes. We show how this role is determined by the atomic structure of the defects, the electronic defect states, and/or the ion transport properties of the defects. The electronic structure of the systems in different resistance states is described in the light of the chemical bonds involved. While for phase change alloys the interplay of ionicity and hybridization in the crystalline and in the amorphous phase determine the resistances, the local redox reaction at the site of extended defects, the change in the oxygen stoichiometry, and the resulting change in the occupancy of relevant orbitals play the major role in transition metal oxides which switch by the thermochemical and the valence change mechanism. Phase transformations are not only discussed for phase change alloys but also for redox-related switching processes. The switching kinetics as well as the ultimate scalability of switching cells are related to structural defects in the materials.
On the Prevalence of „Nonspecific” Binding at the Specific Binding Sites of Globular Proteins (1970)

Strong binding of dyes to simple globular proteins takes place predominantly in areas overlapping the binding sites for substrates, coenzymes and prosthetic groups, in preference to other regions of the protein surface. The structure of the dyes bears no obvious relationship to that of the normal ligands. It is proposed that this phenomenon is a reflection of the special stereochemical features of such sites, their hydrophobicity relative to other portions of the protein surface, and, possibly, greater flexibility in these regions of the protein molecule. The binding properties of antibodies and bovine serum albumin are discussed in relation to this apparent versatility of protein binding sites towards structurally unrelated organic ligands.
Data from Genomic Alterations during the <i>In Situ</i> to Invasive Ductal Breast Carcinoma Transition Shaped by the Immune System (2023)

&lt;div&gt;Abstract&lt;p&gt;The drivers of ductal carcinoma &lt;i&gt;in situ&lt;/i&gt; (DCIS) to invasive ductal carcinoma (IDC) transition are poorly understood. Here, we conducted an integrated genomic, transcriptomic, and whole-slide image analysis to evaluate changes in copy-number profiles, mutational profiles, expression, neoantigen load, and topology in 6 cases of matched pure DCIS and recurrent IDC. We demonstrate through combined copy-number and mutational analysis that recurrent IDC can be genetically related to its pure DCIS despite long latency periods and therapeutic interventions. Immune “hot” and “cold” tumors can arise as early as DCIS and are subtype-specific. Topologic analysis showed a similar degree of pan-leukocyte-tumor mixing in both DCIS and IDC but differ when assessing specific immune subpopulations such as CD4 T cells and CD68 macrophages. Tumor-specific copy-number aberrations in MHC-I presentation machinery and losses in 3p, 4q, and 5p are associated with differences in immune signaling in estrogen receptor (ER)-negative IDC. Common oncogenic hotspot mutations in genes including &lt;i&gt;TP53&lt;/i&gt; and &lt;i&gt;PIK3CA&lt;/i&gt; are predicted to be neoantigens yet are paradoxically conserved during the DCIS-to-IDC transition, and are associated with differences in immune signaling. We highlight both tumor and immune-specific changes in the transition of pure DCIS to IDC, including genetic changes in tumor cells that may have a role in modulating immune function and assist in immune escape, driving the transition to IDC.&lt;/p&gt;Implications:&lt;p&gt;We demonstrate that the &lt;i&gt;in situ&lt;/i&gt; to IDC evolutionary bottleneck is shaped by both tumor and immune cells.&lt;/p&gt;&lt;/div&gt;
Automated Design of FPGAs Facilitated by Cycle-Free Routing (2020)

As device technology advances into the sub-10nm era, the design costs of Field Programmable Gate Arrays (FPGAs) built out of fully-custom, hand-layout blocks have increased dramatically. At the same time, Embedded FPGAs (eFPGAs) are picking up steam in heterogeneous system-on-chip designs, in which case supporting customizable FPGA architectures and reducing design costs are more crucial than squeezing the last bit of performance out of the transistors. To reduce the cost and complexity of FPGA designs, prior works have proposed to build FPGAs using Electronic Design Automation (EDA) tools and standard-cell libraries. Though functionally viable, this approach faces two challenges: 1) An accurate timing model is crucial for FPGA implementation tools to produce correct and optimal results. However, post-layout Static Timing Analysis (STA) with EDA tools is error-prone on FPGAs, because the typical FPGA routing graphs contain many cycles at design time. 2) Conventional FPGA design relies heavily on iterative/empirical improvements to achieve optimal floorplanning and time-budgeting. Without such insights, blocks may be shaped and constrained sub-optimally. This work addresses the first challenge by proposing an algorithm to derive cycle-free sub-graphs. A cycle-free subgraph is achieved by logically ranking the routing tracks and selectively removing some switch block connections. Each subgraph enables accurate, per-switch, post-layout STA, and the union of multiple sub-graphs covers all the timing arcs of the FPGA. Furthermore, our proposed approach addresses the second challenge by enabling the creation of intrinsically cycle-free FPGAs that facilitate a flat multi-block or full-chip design flow. By blending the blocks, the EDA tools can exploit more optimization opportunities and automatically adapt to heterogeneous blocks. Our experiments show that the routability of cycle-free routing graphs is comparable to conventional FPGA routing graphs, and the Quality of Results (QoR) of the FPGA layout is superior to the result of previous approaches.
Linear Aperiodic Array Synthesis Using an Improved Genetic Algorithm (2011)

A novel algorithm on beam pattern synthesis for linear aperiodic arrays with arbitrary geometrical configuration is presented in this paper. Linear aperiodic arrays are attractive for their advantages on higher spatial resolution and lower sidelobe. However, the advantages are attained at the cost of solving a complex non-linear optimization problem. In this paper, we explain the Improved Genetic Algorithm (IGA) that simultaneously adjusts the weight coefficients and inter-sensor spacings of a linear aperiodic array in more details and extend the investigations to include the effects of mutual coupling and the sensitivity of the Peak Sidelobe Level (PSL) to steering angles. Numerical results show that the PSL of the synthesized beam pattern has been successfully lowered with the IGA when compared with other techniques published in the literature. In addition, the computational cost of our algorithm can be as low as 10% of that of a recently reported genetic algorithm based synthesis method. The excellent performance of IGA makes it a promising optimization algorithm where expensive cost functions are involved.
Prediction of pathologic complete response to neoadjuvant systemic therapy in triple negative breast cancer using deep learning on multiparametric MRI (2023)

Triple-negative breast cancer (TNBC) is an aggressive subtype of breast cancer. Neoadjuvant systemic therapy (NAST) followed by surgery are currently standard of care for TNBC with 50-60% of patients achieving pathologic complete response (pCR). We investigated ability of deep learning (DL) on dynamic contrast enhanced (DCE) MRI and diffusion weighted imaging acquired early during NAST to predict TNBC patients' pCR status in the breast. During the development phase using the images of 130 TNBC patients, the DL model achieved areas under the receiver operating characteristic curves (AUCs) of 0.97 ± 0.04 and 0.82 ± 0.10 for the training and the validation, respectively. The model achieved an AUC of 0.86 ± 0.03 when evaluated in the independent testing group of 32 patients. In an additional prospective blinded testing group of 48 patients, the model achieved an AUC of 0.83 ± 0.02. These results demonstrated that DL based on multiparametric MRI can potentially differentiate TNBC patients with pCR or non-pCR in the breast early during NAST.
Distributed Sequential Detection for Gaussian Shift-in-Mean Hypothesis Testing (2015)

This paper studies the problem of sequential Gaussian shift-in-mean hypothesis testing in a distributed multi-agent network. A sequential probability ratio test (SPRT) type algorithm in a distributed framework of the consensus+innovations form is proposed, in which the agents update their decision statistics by simultaneously processing latest observations (innovations) sensed sequentially over time and information obtained from neighboring agents (consensus). For each pre-specified set of type I and type II error probabilities, local decision parameters are derived which ensure that the algorithm achieves the desired error performance and terminates in finite time almost surely (a.s.) at each network agent. Large deviation exponents for the tail probabilities of the agent stopping time distributions are obtained and it is shown that asymptotically (in the number of agents or in the high signal-to-noise-ratio regime) these exponents associated with the distributed algorithm approach that of the optimal centralized detector. The expected stopping time for the proposed algorithm at each network agent is evaluated and is benchmarked with respect to the optimal centralized algorithm. The efficiency of the proposed algorithm in the sense of the expected stopping times is characterized in terms of network connectivity. Finally, simulation studies are presented which illustrate and verify the analytical findings.
Uncontrolled Release of Harmful Microorganisms (1999)

At a recent colloquium held at the U.S. National Academy of Sciences in Washington, DC, there was intensive discussion of a wide range of applications of laboratory automation. These applications included methods for prevention and early detection of biological warfare agents, infectious diseases,
Technical Failure of MR Elastography Examinations of the Liver: Experience from a Large Single-Center Study (2017)

Purpose To assess the determinants of technical failure of magnetic resonance (MR) elastography of the liver in a large single-center study. Materials and Methods This retrospective study was approved by the institutional review board. Seven hundred eighty-one MR elastography examinations performed in 691 consecutive patients (mean age, 58 years; male patients, 434 [62.8%]) in a single center between June 2013 and August 2014 were retrospectively evaluated. MR elastography was performed at 3.0 T (n = 443) or 1.5 T (n = 338) by using a gradient-recalled-echo pulse sequence. MR elastography and anatomic image analysis were performed by two observers. Additional observers measured liver T2* and fat fraction. Technical failure was defined as no pixel value with a confidence index higher than 95% and/or no apparent shear waves imaged. Logistic regression analysis was performed to assess potential predictive factors of technical failure of MR elastography. Results The technical failure rate of MR elastography at 1.5 T was 3.5% (12 of 338), while it was higher, 15.3% (68 of 443), at 3.0 T. On the basis of univariate analysis, body mass index, liver iron deposition, massive ascites, use of 3.0 T, presence of cirrhosis, and alcoholic liver disease were all significantly associated with failure of MR elastography (P < .004); but on the basis of multivariable analysis, only body mass index, liver iron deposition, massive ascites, and use of 3.0 T were significantly associated with failure of MR elastography (P < .004). Conclusion The technical failure rate of MR elastography with a gradient-recalled-echo pulse sequence was low at 1.5 T but substantially higher at 3.0 T. Massive ascites, iron deposition, and high body mass index were additional independent factors associated with failure of MR elastography of the liver with a two-dimensional gradient-recalled-echo pulse sequence. <sup>©</sup> RSNA, 2017.