gebhart/patrepeval huggingface dataset:
Blood‐based biopsies—clinical utility beyond circulating tumor cells (2018)

Circulating tumor cells (CTCs), epithelial-mesenchymal transition (EMT) cells, as well as a number of circulating cancer stromal cells (CStCs) are known to shed into the blood of cancer patients. Individually, and together, these cells provide biological and clinical information about the cancers. Filtration is a method used to isolate all of these cells, while eliminating red and white blood cells from whole peripheral blood. We have previously shown that accurate identification of these cell types is paramount to proper clinical assessment by describing the overlapping phenotypes of CTCs to one such CStC, the cancer-associated macrophage-like cell (CAML). We report that CAMLs possess a number of parallel applications to CTCs but have a broader range of clinical utility, including cancer screening, companion diagnostics, diagnosis, prognosis, monitoring of treatment response, and detection of recurrence. © 2018 The Authors. Cytometry Part A published by Wiley Periodicals, Inc. on behalf of ISAC.
Induction of Differentiation in Acute Promyelocytic Leukemia Cells by 9-cis Retinoic Acid α-Tocopherol Ester (9-cisTretinoin Tocoferil) (1998)

Acute promyelocytic leukemia (APL) has a specific genetic rearrangement between the retinoic acid receptor (RAR)-alpha gene and the pml nuclear protein gene. All-trans retinoic acid (ATRA) induces granulocytic differentiation of APL-derived cells and is used to treat APL patients. However, ATRA interacts with normal cells with RAR throughout the entire body, and when used at high doses or over a long duration, it induces several adverse effects. The development of drugs that selectively act on APL cells may contribute to increasing the therapeutic efficacy of APL treatment as well as elucidating the mechanisms of response to ATRA. In this study, 9-cis retinoic acid alpha-tocopherol ester (9CTT) inhibited the proliferation of APL-derived NB4 and HT93 cells and induced differentiation markers, such as granulocytic maturation, nitroblue tetrazolium reduction, and CD11b expression, in these cells. The effects of 9CTT on non-APL cells, including HL-60 and U937 cells, were much weaker than those on APL cells, and tretinoin tocoferil (TT), which is an alpha-tocopherol ester of ATRA, did not induce the differentiation of APL cells as effectively as 9CTT. The differentiation-inducing effects of 9CTT were inhibited by RAR antagonists. 9CTT and TT similarly induced the transactivating activity of RARs, but were not effective on RXRs. 9CTT downregulated the expression of PML/RAR-alpha protein more effectively than TT, which suggests that it may be involved in the selectivity of 9CTT against APL cells. Interestingly, 9CTT enhanced the differentiation of APL cells induced by ATRA, 9-cis retinoic acid, and synthetic retinobenzoic acids. Combined with 1alpha,25-dihydroxyvitamin D3 (VD3), 9CTT also more than additively induced the differentiation of APL cells. Thus, 9CTT, alone or in combination with other retinoids or VD3, may be useful for the treatment of APL.
Chemical modification of magneto-optic garnet film properties (1994)

Single-crystal magneto-optic garnet films of composition (BiTm)3(FeGa)5O12 have applications to spatial light modulators, optical isolators, and magnetic-field sensors. These as-grown films have a coercivity under 1 Oe and can support cm-size stable domains. It has been found that chemical treatments with oxidizing or reducing gases can reversibly modify the magnetic properties. Treatments are performed at 400–700 °C for fixed times. Reducing treatments dilate the x-ray lattice constant up to 0.1%, introduce Fe2+ monitored by increased optical absorption at 1.00–1.06 μm and decrease Faraday rotation about 5% over the visible spectrum. Oxidation can partially or totally reverse these parameters. Magnetic measurements on the bulk film show that coercivity can be finely controlled, square hysteresis loops attained, and domain-wall mobility changed. At the same time the initial perpendicular anisotropy Hk of 8–12 kOe is decreased while the saturation magnetization (4πMs) of 100–150 G is affected to a minor degree. For magneto-optic imaging of defects, the resolution, contrast, and device operation are assisted favorably. Magnetic measurements are presented as a function of specific chemical treatment. The data suggest that an oxygen vacancy mechanism is operative at the film surface layers.
Discovery of MK-5172, a Macrocyclic Hepatitis C Virus NS3/4a Protease Inhibitor (2012)

A new class of HCV NS3/4a protease inhibitors containing a P2 to P4 macrocyclic constraint was designed using a molecular modeling-derived strategy. Building on the profile of previous clinical compounds and exploring the P2 and linker regions of the series allowed for optimization of broad genotype and mutant enzyme potency, cellular activity, and rat liver exposure following oral dosing. These studies led to the identification of clinical candidate 15 (MK-5172), which is active against genotype 1-3 NS3/4a and clinically relevant mutant enzymes and has good plasma exposure and excellent liver exposure in multiple species.
Nitrite Anion Therapy Protects Against Chronic Ischemic Tissue Injury in <i>db/db</i> Diabetic Mice in a NO/VEGF-Dependent Manner (2013)

Nitrite anion has been demonstrated to be a prodrug of nitric oxide (NO) with positive effects on tissue ischemia/reperfusion injury, cytoprotection, and vasodilation. However, effects of nitrite anion therapy for ischemic tissue vascular remodeling during diabetes remain unknown. We examined whether sodium nitrite therapy altered ischemic revascularization in BKS-Lepr(db/db) mice subjected to permanent unilateral femoral artery ligation. Sodium nitrite therapy completely restored ischemic hind limb blood flow compared with nitrate or PBS therapy. Importantly, delayed nitrite therapy 5 days after ischemia restored ischemic limb blood flow in aged diabetic mice. Restoration of blood flow was associated with increases in ischemic tissue angiogenesis activity and cell proliferation. Moreover, nitrite but not nitrate therapy significantly prevented ischemia-mediated tissue necrosis in aged mice. Nitrite therapy significantly increased ischemic tissue vascular endothelial growth factor (VEGF) protein expression that was essential for nitrite-mediated reperfusion of ischemic hind limbs. Nitrite significantly increased ischemic tissue NO bioavailability along with concomitant reduction of superoxide formation. Lastly, nitrite treatment also significantly stimulated hypoxic endothelial cell proliferation and migration in the presence of high glucose in an NO/VEGF-dependent manner. These results demonstrate that nitrite therapy effectively stimulates ischemic tissue vascular remodeling in the setting of metabolic dysfunction that may be clinically useful.
PenLight (2009)

Digital pen systems, originally designed to digitize annotations made on physical paper, are evolving to permit a wider variety of applications. Although the type and quality of pen feedback (e.g., haptic, audio, and visual) have a huge impact on advancing the digital pen technology, dynamic visual feedback has yet to be fully investigated. In parallel, miniature projectors are an emerging technology with the potential to enhance visual feedback for small mobile computing devices. In this paper we present the PenLight system, which is a testbed to explore the interaction design space and its accompanying interaction techniques in a digital pen embedded with a spatially-aware miniature projector. Using our prototype, that simulates a miniature projection (via a standard video projector), we visually augment paper documents, giving the user immediate access to additional information and computational tools. We also show how virtual ink can be managed in single and multi-user environments to aid collaboration and data management. User evaluation with professional architects indicated promise of our proposed techniques and their potential utility in the paper-intensive domain of architecture.
Phase-shifting mask polarimetry: monitoring polarization at <inline-formula><math display="inline" altimg="none" overflow="scroll"><mrow><mn>193</mn><mtext>-</mtext><mi>nm</mi></mrow></math></inline-formula> high numerical aperture and immersion lithography with phase shifting masks (2005)

A technique using phase-shifting test mask patterns is introduced for monitoring polarization balance of the illumination in high numerical aperture (NA) and immersion projection printing systems. Test mask patterns are derived from high NA proximity effects and serve to scatter light into high angle spatial frequencies. This creates a central intensity dependent only on the local state of polarization. A test mask consisting of multiple patterns is proposed to monitor the polarization from any arbitrary illumination scheme. Proper calibration of the test reticle enables reasonable mask-making limitations and mask topography effects to be tolerated. A set of linear equations enable determination of the Stokes parameters from a series of resist images. Practical examples are simulated with rigorous electromagnetic theory. In resist, this technique is likely to monitor polarization with a sensitivity of more than 1.5% of the clear field per percent change in polarization state for on-axis illumination, or more than 0.75% for off-axis illumination. The effects of various realistic imaging conditions are discussed.
Biotechnological application of functional genomics towards plant‐parasitic nematode control (2011)

Plant-parasitic nematodes are primary biotic factors limiting the crop production. Current nematode control strategies include nematicides, crop rotation and resistant cultivars, but each has serious limitations. RNA interference (RNAi) represents a major breakthrough in the application of functional genomics for plant-parasitic nematode control. RNAi-induced suppression of numerous genes essential for nematode development, reproduction or parasitism has been demonstrated, highlighting the considerable potential for using this strategy to control damaging pest populations. In an effort to find more suitable and effective gene targets for silencing, researchers are employing functional genomics methodologies, including genome sequencing and transcriptome profiling. Microarrays have been used for studying the interactions between nematodes and plant roots and to measure both plants and nematodes transcripts. Furthermore, laser capture microdissection has been applied for the precise dissection of nematode feeding sites (syncytia) to allow the study of gene expression specifically in syncytia. In the near future, small RNA sequencing techniques will provide more direct information for elucidating small RNA regulatory mechanisms in plants and specific gene silencing using artificial microRNAs should further improve the potential of targeted gene silencing as a strategy for nematode management.
High bit rate and reduced noise multiwavelength modelocked semiconductor lasers (2003)

A gain-flattened multiwavelength modelocked semiconductor laser transmitter generates 6 Gb/s pulses into 168 discrete wavelength channels. Hybrid modelocking suppresses mode partition noise and produces error-free (pulse Q > 13) pulses simultaneously in each channel of a multiwavelength semiconductor laser.
Scaling diode-pumped Nd<sup>3+</sup>and Yb<sup>3+</sup>-doped YCa 4 O(BO 3 ) 3 (YCOB) self-frequency doubling lasers (2000)

The development of didoe-pumped self-frequency doubling (SFD) YCA<SUB>4</SUB>O(BO<SUB>3</SUB>)<SUB>3</SUB> (YCOB) crystals doped with ND<SUP>3+</SUP> or YB<SUP>3+</SUP> ions offers an attractive alternative to traditional intra-cavity doubling techniques using a separate non-linear crystal. Here, we summarize the progress of scaling SFD lasers to higher powers. Moreover, we examine the potential and limitations of these devices. While SFD lasers are potentially more compact and less costly, scaling to higher powers in the visible region requires careful assessment of mode matching and cavity mode brightness. Combining optical gain and frequency conversion in the same material requires a compromise between the ideal cavity mode for mode matching and generating the largest available power density of the laser mode for optimum frequency doubling. The lack of adjustment of the cavity mode inherently limits scaling of SFD laser operation when using low brightness high power laser diodes. We have employed a new source developed by Polaroid Corp. using multiple high-brightness laser diodes to investigate the potential of increasing SFD laser output. We have then compared the efficiency of this novel pump technique to a single diode pumped system to determine the importance of brightness of the pump source to SFD operation.
Progressive Pulse Compression: A Novel Technique for Blind Range Recovery for Solid-State Radars (2021)

Abstract In this paper, a novel technique is proposed to mitigate the so-called blind range on radars that use pulse compression. It is well known that the blind range is caused by the strong leak-through into the receiver during the transmission cycle. The proposed technique is called progressive pulse compression (PPC) and is based on partial decoding. PPC uses a portion of the uncontaminated received signal in conjunction with pulse compression to estimate the echoes from the incomplete signal. The technique does not require the use of a fill pulse or any hardware modifications. PPC can be divided into three steps. The fist step is to discard all the received signals during the transmit cycle and apply a smooth taper for continuous transition from zero to one. The second step is to perform the pulse compression using matched filter. The combination of these two steps is equivalent to performing pulse compression using a progressively changing template to partially extract the uncontaminated received signal for compression. The third step is to compensate for the progressively changing template so that proper reflectivity values can be recovered. This technique has been tested on the PX-1000 and will be implemented on PX-10k in the near future. These two radars are designed and operated by the Advanced Radar Research Center at the University of Oklahoma and are both X-band software-defined solid-state systems. The results presented in this paper are collected using the PX-1000 radar.
Metallic‐Glass Nanostructures: Tunable Hierarchical Metallic‐Glass Nanostructures (Adv. Funct. Mater. 21/2013) (2013)

Palladium-rich nanostructures with widely different morphologies are obtained by electrochemical processing of a nickel-palladium metallic glass. Metallic glasses are multicomponent alloys that exist in a wide range of chemical compositions and have a fully amorphous structure. On page 2708, Sundeep Mukherjee and co-workers report that starting with a homogeneous and isotropic amorphous surface, the morphology and chemistry can be modified to obtain hierarchical nanostructures with high catalytic activity.
Slowing the titration rate of tramadol HCl reduces the incidence of discontinuation due to nausea and/or vomiting: a double-blind randomized trial (1999)

This study demonstrated that a slower titration rate of tramadol HCl improves tolerability in patients who previously discontinued therapy due to nausea and/or vomiting. This study also demonstrates that the rate of titration of tramadol HCl rather than the target dose is the major determinant of tolerability.
Increased dialyzer reuse with citrate dialysate (2005)

Dialyzer reuse is limited by the clotting of blood, which blocks the fibers and reduces the membrane surface area. Clotting during treatment may also reduce dialysis efficiency and potentially decrease delivered dose, Kt/V(urea). A new dialysate containing citric acid, instead of the standard acetic acid, as the acidifying agent has become available and is associated with reduced clotting during acute dialysis treatments. The effect of citric acid dialysate on dialyzer reuse was evaluated in this prospective, controlled, multicenter study involving maintenance hemodialysis patients. A total of 105 patients from five dialysis units were switched to the new dialysate and new dialyzers. Reuse outcome on the new dialysate was compared with the reuse on the regular acetic acid containing bicarbonate dialysate (controls). The overall reuse with citrate dialysate increased significantly from 15.1 +/- 9.4 to 18 +/- 10.0 (mean +/- SD) on regular and citrate dialysate, respectively (p = 0.0003). The most significant increase was seen in those patients who had limited reuse before the switch to citrate dialysate; 51, 59, and 134% increases occurred in those with 10 to 15, 5 to 10, and < 5 reuses at controls, respectively. Interestingly, the 10 patients with 10 or fewer reuses had significantly lower Kt/V(urea) at baseline (before the switch to citric acid dialysate) than those with > 10 reuses (1.23 +/- 0.23 vs. 1.47 +/- 0.23, respectively, p = 0.009). The Kt/V(urea) increased to 1.41 +/- 0.31 after the switch in the low-reuse group but the increase did not reach statistical significance (p = 0.07). The results from this study show that citric acid-containing dialysate is associated with increase in dialyzer reuse and appears to be related to reduced clotting.
Adaptive interpolation with flexible filter structures for video coding (2009)

Two novel algorithms are proposed for improving the coding efficiency of adaptive interpolation schemes for video codecs, without increasing implementation complexity. Proposed algorithms utilize two different filter structures with equal tap length, but with complementary frequency responses. Depending on the content being coded, encoder selects which one of the two filter structure is optimal and signals this information to the decoder. In addition, the symmetry of filters is not pre-defined but is flexible. Encoder selects the optimal filter symmetry depending on the coding rate and the content and signals this information to the decoder. Experimental results show, that proposed improvements bring up to 7% of bit-rate reduction at high bit-rate over conventional adaptive interpolation. When compared to H.264/AVC, average gain over the test set is 11%. Coding efficiency is improved without increasing the complexity, thus proposed algorithms are suitable for mobile multimedia use-cases, where the computational resources are very limited.
Terahertz Light Sources by Electronic-Oscillator-Driven Second-Harmonic Generation in Cavities Featuring Extreme Confinement (2022)

The majority of sources of coherent optical radiation rely on laser oscillators driven by population inversion. Despite their technological importance in communications, medicine, industry, and other fields, it remains a challenge to access the spectral range of 0.1--10 THz (the ``terahertz gap''), a frequency band for applications ranging from spectroscopy to security and high-speed wireless communications. Here, we propose a way to produce coherent radiation spanning the THz gap by efficient second-harmonic generation in low-loss dielectric structures, starting from technologically mature electronic oscillators in the approximately 100 GHz range. To achieve this goal, we introduce hybrid THz-band dielectric cavity designs that combine (1) extreme field concentration in high-quality-factor resonators with (2) nonlinear materials enhanced by phonon resonances. We theoretically predict conversion efficiencies of $>{10}^{3}\mathrm{%}/$W and the potential to bridge the THz gap with 1 W of input power. This approach enables efficient, cascaded parametric frequency converters, and light sources extensible into the mid-IR spectrum and beyond.
Rendering of 3D-wavelet-compressed concentric mosaic scenery with progressive inverse wavelet synthesis (PIWS) (2000)

The concentric mosaics offer a quick solution to the construction and navigation of a virtual environment. To reduce the vast data amount of the concentric mosaics, a compression scheme based on 3D wavelet transform has been proposed in a previous paper. In this work, we investigate the efficient implementation of the renderer. It is preferable not to expand the compressed bitstream as a whole, so that the memory consumption of the renderer can be reduced. Instead, only the data necessary to render the current view are accessed and decoded. The progressive inverse wavelet synthesis (PIWS) algorithm is proposed to provide the random data access and to reduce the calculation for the data access requests to a minimum. A mixed cache is used in PIWS, where the entropy decoded wavelet coefficient, intermediate result of lifting and fully synthesized pixel are all stored at the same memory unit because of the in- place calculation property of the lifting implementation. PIWS operates with a finite state machine, where each memory unit is attached with a state to indicate what type of content is currently stored. The computational saving achieved by PIWS is demonstrated with extensive experiment results.
Bias-Free Branch Predictor (2014)

Prior research in neutrally-inspired perceptron predictors and Geometric History Length-based TAGE predictors has shown significant improvements in branch prediction accuracy by exploiting correlations in long branch histories. However, not all branches in the long branch history provide useful context. Biased branches resolve as either taken or not-taken virtually every time. Including them in the branch predictor's history does not directly contribute any useful information, but all existing history-based predictors include them anyway. In this work, we propose Bias-Free branch predictors theatre structured to learn correlations only with non-biased conditional branches, aka. Branches whose dynamic behaviorvaries during a program's execution. This, combined with a recency-stack-like management policy for the global history register, opens up the opportunity for a modest history length to include much older and much richer context to predict future branches more accurately. With a 64KB storage budget, the Bias-Free predictor delivers 2.49 MPKI (mispredictions per1000 instructions), improves by 5.32% over the most accurate neural predictor and achieves comparable accuracy to that of the TAGE predictor with fewer predictor tables or better accuracy with same number of tables. This eventually will translate to lower energy dissipated in the memory arrays per prediction.
Radiation dose distributions in three dimensions from tomographic optical density scanning of polymer gels: I. Development of an optical scanner (1996)

A new method of dosimetry of ionizing radiations has been developed that makes use of tissue-equivalent polymer gels which are capable of recording three-dimensional dose distributions. The dosimetric data stored within the gels are measured using optical tomographic densitometry. The dose-response mechanism relies on the production of light scattering microparticles which result from the polymerization of acrylic comonomers dispersed in the gel. The attenuation of a collimated light beam caused by scattering in the irradiated optically turbid medium is directly related to the radiation dose over the range 0-10 Gy. An optical scanner has been developed which incorporates an He-Ne laser, photodiode detectors, and a rotating gel platform. Using mirrors mounted on a translating stage, the laser beam scans across the gel between each incremental rotation of the platform. Using the set of optical density projections obtained, a cross sectional image of the radiation field is then reconstructed. Doses in the range 0-10 Gy can be measured to better than 5% accuracy with a spatial resolution approximately 2 mm using the current prototype scanner. This method can be used for the determination of three-dimensional dose distributions in irradiated gels, including measurements of the complex distributions produced by multi-leaf collimators, dynamic wedge and stereotactic treatments, and for quality assurance procedures.