gebhart/patrepeval huggingface dataset:
Protein activation mapping and exploratory predictive markers for pCR in triple-negative breast cancer patients treated with neratinib in the I-SPY 2 TRIAL. (2015)

1085 Background: In the I-SPY 2 trial, the pan-ERBB inhibitor, neratinib (N) arm was open to all HR/HER2 subtypes but graduated in the HR-/HER2+ signature. Exploratory analysis of protein signaling was performed to identify biomarker candidates correlated with pCR in the TN population. We evaluated 110 key signaling proteins using reverse phase protein microarray (RPPA) data from pre-treatment LCM purified tumor epithelium. Methods: Of 59 TN patients, 49 (N: 30, concurrent controls: 19) had RPPA and pCR data. RPPA data was correlated to pCR in both the treated and untreated patients using parametric (t-test) or non-parametric (Wilcoxon) statistical analysis, depending on data distribution. Only analytes whose levels were associated with response in the N but not the control arm were selected for further analysis. Markers are analyzed individually; p-values are descriptive and were not corrected for multiple comparisons. ROC analysis identified an optimal cut point and pCR rates of biomarker positive patients were assessed using that cut point. Results: Out of 110 analytes analyzed, only activation of HER2 Y1248, p = 0.03; EGFR Y1173, p = 0.009; were found to be positive predictors of pCR, and 3 proteins, TIE2 Y992, p = 0.02; LC3B, p = 0.02, and A-RAF S299, p = 0.0008, were found to be negative predictors of pCR. pCR rates in the biomarker positive group of 62.5% (10/16), 66% (11/16), 55%(10,/18), 67% (12/17). 61% (11/18) were determined for phospho- HER2, EGFR, TIE2, A-RAF and total LC3B, respectively, compared to a pCR rate of 40% ffor the IHC/FISH-based TN subgroup where RPPA data were available. Conclusions: Our sample size is too small to draw definitive conclusions. However, activation of HER2-EGFR in HER2- tumors may identify patients who respond to N. Low levels of activated A-RAF and LC3B also correlated with response. The results imply that there is a subset TN patients that paradoxically exhibit HER family signaling activation and may achieve clinical benefit with N. These findings merit future consideration as we develop trials for patients with suboptimal response to neoadjuvant therapy where biomarkers could be used as the basis for treatment reassignment. Clinical trial information: NCT01042379.
Curing Color Blindness--Mice and Nonhuman Primates (2014)

It has been possible to use viral-mediated gene therapy to transform dichromatic (red-green color-blind) primates to trichromatic. Even though the third cone type was added after the end of developmental critical periods, treated animals acquired red-green color vision. What happened in the treated animals may represent a recapitulation of the evolution of trichromacy, which seems to have evolved with the acquisition of a third cone type without the need for subsequent modification to the circuitry. Some transgenic mice in which a third cone type was added also acquired trichromacy. However, compared with treated primates, red-green color vision in mice is poor, indicating large differences between mice and monkeys in their ability to take advantage of the new input. These results have implications for understanding the limits and opportunities for using gene therapy to treat vision disorders caused by defects in cone function.
Time-stretched short time Fourier transform (2004)

We propose and demonstrate time-stretched short-time Fourier transform (TS-STFT) to overcome the limitation of analog to digital converter (ADC) in time-frequency analysis of nonstationary signals. Experimentally, time-frequency analysis of highly chirped RF signals with chirp rate as high as 350 GHz/ns is demonstrated. An effective real-time sampling rate of 320 GSa/s is achieved. In our TS-STFT system, first ultra short window is applied on highly chirped signals. Then the window is stretched in time by photonic time stretch technique to allow its capture by the ADC to perform STFT in digital domain. This method enhances the analog bandwidth and effective sampling rate of the sampling ADC and enable us realize the instantaneous behavior of highly chirped ultra fast signal.
Surgery and Sample Processing for Correlative Imaging of the Murine Pulmonary Valve (2021)

The underlying causes of heart valve related-disease (HVD) are elusive. Murine animal models provide an excellent tool for studying HVD, however, the surgical and instrumental expertise required to accurately quantify the structure and organization across multiple length scales have stunted its advancement. This work provides a detailed description of the murine dissection, en bloc staining, sample processing, and correlative imaging procedures for depicting the heart valve at different length scales. Hydrostatic transvalvular pressure was used to control the temporal heterogeneity by chemically fixing the heart valve conformation. Micro-computed tomography (µCT) was used to confirm the geometry of the heart valve and provide a reference for the downstream sample processing needed for the serial block face scanning electron microscopy (SBF-SEM). High-resolution serial SEM images of the extracellular matrix (ECM) were taken and reconstructed to provide a local 3D representation of its organization. µCT and SBF-SEM imaging methods were then correlated to overcome the spatial variation across the pulmonary valve. Though the work presented is exclusively on the pulmonary valve, this methodology could be adopted for describing the hierarchical organization in biological systems and is pivotal for the structural characterization across multiple length scales.
The Prevention of Prostate Cancer — The Dilemma Continues (2003)

Prostate cancer is the most common non-skin cancer in the United States, the second leading cause of death from cancer among U.S. men, and the seventh leading cause of death in the United States. The number of new cases of prostate cancer, now estimated at more than 220,000 per year, is expected to increase to more than 380,000 by 2025 because of the aging male population. The incidence of prostate cancer and the rate of death due to the disease increase exponentially with age. The other major risk factors for prostate cancer include a family history of prostate cancer, black . . .
Motion interpolation by optimal control (1988)

Motion Interpolation, which arises in many situations such as Keyframe Animation , is the synthesis of a sequence of images portraying continuous motion by interpolating between a set of keyframes . If the keyframes are specified by parameters of moving objects at several instants of time, (e.g., position, orientation, velocity) then the goal is to find their values at the intermediate instants of time. Previous approaches to this problem have been to construct these intermediate, or in-between , frames by interpolating each of the motion parameters independently. This often produces unnatural motion since the physics of the problem is not considered and each parameter is obtained independently. Our approach models the motion of objects and their environment by differential equations obtained from classical mechanics. In order to satisfy the constraints imposed by the keyframes we apply external control. We show how smooth and natural looking interpolations can be obtained by minimizing a combination of the control energy and the roughness of the trajectory of the objects in 3D-space. A general formulation is presented which allows several trade-offs between various parameters that control motion. Although optimal parameter values resulting in the best subjectively looking motion are not yet known, our simulations have produced smooth and natural motion that is subjectively better than that produced by other interpolation methods, such as the cubic splines.
Hollow and sulfonated microporous organic polymers: versatile platforms for non-covalent fixation of molecular photocatalysts (2015)

Sulfonated hollow microporous organic polymers showed excellent heterogenization ability towards various cationic photocatalysts through ionic interaction.
Solid state qubits: how learning from CMOS fabrication can speed-up progress in Quantum Computing (2021)

Building quantum computers requires not only a large number of qubits with high fidelity and low variability, but also a large amount of analog and digital components to drive the qubits. Larger arrays of solid-state qubits with high fidelity and low variability require improvements in fabrication processes and array layout design co-optimized with the underlying hardware technology. Here we outline progress on 300mm fabrication of qubit devices and on classical CMOS components to enable the quantum system. We describe work on superconducting qubits and spin qubits in Si, both types of devices fabricated on 300mm experimental platforms and discuss challenges related to variability. Massive electrical characterization is key over wide temperature range is key to enabling system upscaling for QC.
The synergistic binding of anions and Fe3+ by transferrin. Implications for the interlocking sites hypothesis. (1975)

The finding that transferrin does not bind Fe3+ at the specific metal binding sites in the absence of carbonate and synergistic anions emphasizes the fundamental importance of the anion binding site to the chemistry of Fe3+-transferrin-CO32-. An important question regards the chemical and structural requirements for carbonate substitution. This has been, however, an area of some dispute in the literature. We have utilized four synthetic routes for the preparation of Fe3+-transferrin-anion complexes. The products have been examined with regard to spectral properties, and reaction with: (a) NaHCO3, (b) Fe3+-nitrilotriacetic acid in NaHCO3, and (c) sodium citrate under CO2-free conditions. The results provide information as to which anions are synergistic, and the basic properties of the Fe3+-transferrin-anion complexes that are formed. The 6 inorganic anions that were tested were all found to be nonsynergistic. Dihydroxyacetone and glyceraldehyde were also nonsynergistic. Dicarboxylic acids were found to form stable Fe3+-transferrin-anion complexes which were only slowly displaced by carbonate. Several monocarboxylic acids with proximal aldehyde, ketone, alcohol, amino, or thiol functional groups proved to be synergistic. CPK molecular model studies suggested the functional group and the carboxylic acid must be able to fit within a site between 6.3 and 7.0 A in maximal length. One large substituent could be accommodated by the site, however, two methylgroups on the alpha carbon to a carboxylate group could not be accommodated. Chloroacetate and monocarboxylic acids were nonsynergistic. The results are interpreted in terms of an interlocking sites hypothesis which envisions the synergistic anion as interacting with the protein via its its carboxyl group and bonding with the Fe3+ via its proximal functional group.
Vaccination as immunotherapy for B cell lymphoma (1997)

Current therapy does not cure the majority of patients with B cell non-Hodgkin's lymphoma (NHL) and further intensification does not benefit the patient. Therefore, new approaches are necessary. Immunotherapy has become again a major interest as a new treatment modality for B cell lymphoma since the discovery that the lymphoma specific Id can be presented to antigen-specific T cells. Vaccination of the tumour-bearing host is one of the major strategies to induce a T cell mediated anti-tumour immunity in vivo. For B cell lymphomas the lymphoma specific Id can be used as a tumour-specific antigen to stimulate T cells. Alternatively, the malignant B cells can be modified to become efficient antigen presenting cells (APCs) and present peptides from their own tumour-specific antigens to the autologous T cells. Currently explored and future vaccination strategies for B cell lymphoma will be discussed here.
Asymmetric Stereodivergent Strategy Towards Aminocyclitols (2014)

A concise asymmetric synthesis of aminocyclitols, such as diastereomeric 2-deoxystreptamine analogues and conduramine A, is described. The Pd-catalyzed asymmetric desymmetrization of meso 1,4-dibenzolate enables the synthesis of highly oxidized cyclohexane architectures. These scaffolds can potentially be used to access new aminoglycoside antibiotics and enantiomerically pure α-glucosidase inhibitors.
ChemInform Abstract: 3‐(Tetrahydropyridinyl)indoles. (1996)

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.
Enhanced and polarized emission from single colloidal CdSe/CdS nanocrystals coupled to a one-dimensional gold grating (2016)

We present in detail the fluorescence properties of single thick-shell CdSe/CdS colloidal nanocrystals coupled to a linear one-dimensional gold grating. In addition to the photoluminescence decay rate increase, we point out that the polarization ratio of the emission is dramatically enhanced. It overcomes 80% and can reach values close to unity. Experimental results are successfully compared to theoretical predictions. Blinking suppression is also reported.
Performance analysis of Internet gateway discovery protocols in ad hoc networks (2004)

When an ad hoc network is connected to the Internet, it is important for the mobile nodes to detect the available gateways providing access to the Internet. Therefore, a gateway discovery mechanism is required. The two main approaches for discovering Internet gateways are the reactive and the proactive one. This paper compares the performance of these approaches in various scenarios by means of simulation. We show that the proactive approach performs better in the simulated scenario.
Deep Neural Network for Robust Modulation Classification Under Uncertain Noise Conditions (2019)

Recently, classifying the modulation schemes of signals using deep neural network has received much attention. In this paper, we introduce a general model of deep neural network (DNN)-based modulation classifiers for single-input single-output (SISO) systems. Its feasibility is analyzed using maximum a posteriori probability (MAP) criterion and its robustness to uncertain noise conditions is compared to that of the conventional maximum likelihood (ML)-based classifiers. To reduce the design and training cost of DNN classifiers, a simple but effective pre-processing method is introduced and adopted. Furthermore, featuring multiple recurrent neural network (RNN) layers, the DNN modulation classifier is realized. Simulation results show that the proposed RNN-based classifier is robust to the uncertain noise conditions, and the performance of it approaches to that of the ideal ML classifier with perfect channel and noise information. Moreover, with a much lower complexity, it outperforms the existing ML-based classifiers, specifically, expectation maximization (EM) and expectation conditional maximization (ECM) classifiers which iteratively estimate channel and noise parameters. In addition, the proposed classifier is shown to be invariant to the signal distortion such as frequency offset. Furthermore, the adopted pre-processing method is shown to accelerate the training process of our proposed classifier, thus reducing the training cost. Lastly, the computational complexity of our proposed classifier is analyzed and compared to other traditional ones, which further demonstrates its overall advantage.
Charge‐Selective Contact Materials for Perovskite Solar Cells (<scp>PSCs</scp>) (2018)

This chapter attempts to give a systematic introduction about the choices of both electron- and hole-selective contact materials for efficient perovskite solar cells (PSCs). A huge number of hole-selective electron-blocking materials (HTMs) have been synthesized for PSCs, which can be generally divided into organic and inorganic HTMs. In typical PSCs, the electron-selective contact material (ETM) is responsible for selective extraction of electrons at the anode contact, adopted from dye-sensitized solar cells (DSSCs) and blocking holes from recombination with injected electrons. Similar to its counterpart HTM, the ETM can be divided into inorganic ETM, organic ETM, and composite ETM depending on the nature of the material. It is desirable that selective contact materials have larger bandgaps than that of perovskite films to avoid the excitons from recombining at the electrode. Also, it is crucial to design and synthesize selective contact materials with high conductivity to reduce the series resistance of the PSCs.
Continuous wave terahertz photomixing in low-temperature InGaAs (2006)

Highly-resistive low-temperature grown InGaAs, with a sub-500 fs carrier lifetime, is used as an all-optoelectronic continuous-wave terahertz photomixer system based on diode lasers. Interdigitated electrodes fabricated on epitaxial low-temperature grown In/sub 0.3/Ga/sub 0.7/As are used as photomixers to generate and detect radiation from microwave frequencies (<100 GHz) to beyond 1.0 THz.
Polarisation (2011)

ZusammenfassungIn den vorangegangenen Kapiteln haben wir Licht immer wieder als elektromagnetische Welle betrachtet, die wir durch das elektrische Feld \(\vec{E}\) und den magnetischen Fluss \(\vec{B}\) beschrieben haben. In diesem Kapitel werden wir uns normalerweise auf die Orientierung des elektrischen Feldes zur Charakterisierung der Welle beschränken, da \(\vec{B}\) aber immer senkrecht auf \(\vec{E}\) steht, geht dadurch keine Information verloren.
Integrated Multi-view 3D Image Capture and Motion Parallax 3D Display System (2022)

We propose an integrated 3D image capture and display system using a transversely moving camera, regular 2D display screen and user tracking that can facilitate the multi-view capture of a real scene or object and display the captured perspective views in 3D. The motion parallax 3D technique is used to capture the depth information of the object and display the corresponding views to the user using head tracking. The system is composed of two parts, the first part consists of a horizontally moving camera interfaced with a customized camera control and capture application. The second part consist of a regular LCD screen combined with web camera and user tracking application. The 3D multi-view images captured through the imaging setup are relayed to the display based on the user location and corresponding view is dynamically displayed on the screen based on the viewing angle of the user with respect to the screen. The developed prototype system provides the multi-view capture of 60 views with the step size of 1 cm and greater than 40˚ field-of-view overlap. The display system relays 60 views providing the viewing angle coverage of ±35˚ where the angular difference between two views is 1.2˚.
Time-Resolved Optical Spectroscopy of Wood (2008)

We have proposed and experimentally demonstrated that picosecond time-resolved optical spectroscopy in the visible/near-infrared (NIR) region (700-1040 nm) is a useful technique for noninvasive characterization of wood. This technique has been demonstrated on both softwood and hardwood samples treated in different ways simulating the aging process suffered by waterlogged woods. In all the cases, alterations of absorption and scattering spectra were observed, revealing changes of chemical and structural composition.
Rayleigh backscattering in optical fibers: a noise limitation and a sensing mechanism (1994)

It has become recognised of late that when some of the highly coherent laser sources that are now available are used in reflective-type interferometric systems with long connecting leads, noise due to Rayleigh back-scattering may provide a fundamental limit on the resolution of the sensor.
Uncoupled Anti-HIV and Immune-Enhancing Effects when Combining IFN-α and IL-7 (2005)

Cytokine-based therapies have been examined for purging viral reservoirs and immunomodulation in HIV infection. However, single cytokines did not result in either HIV eradication or an efficient HIV-specific immune response. We hypothesize that cytokines with distinct biologic effects need to be combined for immunotherapy of HIV infection. In this study, we investigated the anti-HIV activity and immune-enhancing effects of the combination of IFN-alpha and IL-7. In human lymphocyte aggregate cultures infected ex vivo with the X4 HIV strain NL4-3, IFN-alpha/IL-7 potently inhibited HIV replication and preserved CD4(+) T cells, probably by up-regulating Bcl-2. IFN-alpha/IL-7 also strongly inhibited R5 HIV replication. Furthermore, in allogeneic MLRs, IFN-alpha/IL-7 increased T cell proliferation and IFN-gamma production. IFN-alpha alone also had strong anti-HIV activity, but neither preserved CD4(+) T cells nor increased T cell responses in MLRs. IL-7 alone maintained T cells and enhanced T cell activation in MLRs, but only moderately inhibited or increased HIV replication. Thus, coadministration of IFN-alpha/IL-7 combines the potent anti-HIV activity of IFN-alpha with the beneficial effects of IL-7 on T cell survival and function. We speculate that IFN-alpha will block viral replication, activate APCs, and up-regulate MHC molecules, thus allowing IL-7 to display its effects for generating an efficient immune response. In this scenario, the known reactivation of latent HIV by IL-7 may be advantageous.
A Model of Full Penetration Arc-Welding for Control System Design (1985)

A model of the dynamics of full penetration welding is presented that relates the heat input to the resulting width of the backbead. It is developed from a heat balance using the pool as a control volume, and is applicable primarily to autogenous gas-tungsten arc welding (GTAW). Two means of modulating the input are considered: 1) varying the torch current and 2) varying the torch travel velocity. The proposed model in both cases is first order, but it has non-constant) parameters (i.e., gain and time constant). Regardless of which input is used, the gain and time constant of the system are shown to depend strongly upon the thickness of the material, the preheat temperature, and the nominal torch velocity. These trends were confirmed in a series of open-loop step tests, where gain and time constant were directly measured, and in closed-lop tests, where step and frequency response methods were used. The resulting model permits rational high performance controller design, and the variable parameters of the system suggest the need for parameter adaptive control.
Evaluating the suitability of hyper- and multispectral imaging to detect foliar symptoms of the grapevine trunk disease Esca in vineyards (2020)

In this study, ground-based hyperspectral and airborne multispectral approaches for the detection of foliar Esca symptoms are presented. Both sensor systems seem to be suitable for the in-field detection of the disease, even though airborne data acquisition has to be further optimized. Our disease detection approaches could facilitate monitoring plant phenotypes in a vineyard.
Radiographic verification of knee goniometry (1986)

The accuracy of knee goniometry was examined by comparing goniometric measurements with radiographic bone angle measurements of six positions of the knee, namely, 0 degree, 15 degrees, 30 degrees, 45 degrees, 60 degrees, and 90 degrees. Within the first 15 degrees of knee flexion joint excursion measured by goniometry differed significantly from bone angle measurement (p less than 0. 01). With 30 degrees of knee flexion or more, no significant difference was found between goniometric measurements and bone angle measurements of knee motion. These findings suggest that within the first 15 degrees of knee flexion, goniometric measurement of joint excursion may be remarkably wrong. On account of this, it was suggested that when range of motion is limited at the knee joint, caution should be exercised in determining movement gains or losses within the initial 15 degrees of knee flexion.