gebhart/patrepeval huggingface dataset:
Folded Integer Multiplication for FPGAs (2021)

Encryption - especially the key exchange algorithms such as RSA - is an increasing use-model for FPGAs, driven by the adoption of the FPGA as a SmartNIC in the datacenter. While bulk encryption such as AES maps well to generic FPGA features, the very large multipliers required for RSA are a much more difficult problem. Although FPGAs contain thousands of small integer multipliers in DSP Blocks, aggregating them into very large multipliers is very challenging because of the large amount of soft logic required - especially in the form of long adders, and the high embedded multiplier count. In this paper, we describe a large multiplier architecture that operates in a multi-cycle format and which has a linear area/throughput ratio. We show results for a 2048-bit multiplier that has a latency of 118 cycles, inputs data every 9th cycle and closes timing at 377MHz in an Intel Arria 10 FPGA, and over 400MHz in a Stratix 10. The proposed multiplier uses 1/9 of the DSP resources typically used in a 2048-bit Karatsuba implementation, showing a perfectly linear throughput to DSP-count ratio. Our proposed solution outperforms recently reported results, in either arithmetic complexity - by making use of the Karatsuba techniques, or in scheduling efficiency - embedded DSP resources are fully utilized.
New SmAPF Mesogens Designed for Analog Electrooptics Applications (2017)

We have previously reported the first realization of an orthogonal ferroelectric bent-core SmAP<sub>F</sub> phase by directed design in mesogens with a single tricarbosilane-terminated alkoxy tail. Given the potentially useful electrooptic properties of this phase, including analog phase-only electrooptic index modulation with optical latching, we have been exploring its "structure space", searching for novel SmAP<sub>F</sub> mesogens. Here, we report two classes of these-the first designed to optimize the dynamic range of the index modulation in parallel-aligned cells by lowering the bend angle of the rigid core, and the second expanding the structure space of the phase by replacing the tricarbosilane-terminated alkyl tail with a polyfluorinated polyethylene glycol oligomer.
Effect of chemical modifications on modulation of gene expression by duplex antigene RNAs that are complementary to non-coding transcripts at gene promoters (2010)

Antigene RNAs (agRNAs) are small RNA duplexes that target non-coding transcripts rather than mRNA and specifically suppress or activate gene expression in a sequence-dependent manner. For many applications in vivo, it is likely that agRNAs will require chemical modification. We have synthesized agRNAs that contain different classes of chemical modification and have tested their ability to modulate expression of the human progesterone receptor gene. We find that both silencing and activating agRNAs can retain activity after modification. Both guide and passenger strands can be modified and functional agRNAs can contain 2'F-RNA, 2'OMe-RNA, and locked nucleic acid substitutions, or combinations of multiple modifications. The mechanism of agRNA activity appears to be maintained after chemical modification: both native and modified agRNAs modulate recruitment of RNA polymerase II, have the same effect on promoter-derived antisense transcripts, and must be double-stranded. These data demonstrate that agRNA activity is compatible with a wide range of chemical modifications and may facilitate in vivo applications.
Fivefold symmetric homonuclear dipolar recoupling in rotating solids: Application to double quantum spectroscopy (1999)

We describe a new fivefold symmetric approach to homonuclear recoupling in rotating solids that is based on rotor-synchronized, spin-lock rf irradiation of the type employed previously in MELODRAMA and C7 (and their derivative sequences) for C13–13C recoupling. The fivefold sequence, like its sevenfold relatives, is γ-encoded, and therefore exhibits a theoretical efficiency of ∼73% for double quantum filtering (2QF). However, since the ratio of rf field strength, ωrf/2π, to spinning frequency, ωr/2π, is lower, it is possible to operate the sequence at higher spinning rates, and we have investigated the 2QF efficiency as a function of H1 decoupling field strength at high spinning frequencies. We observe dramatic oscillations of the recoupled signal with a period ∼ωr/2π indicating that the H1 reservoir is behaving partially inhomogeneously. This kind of double quantum recoupling is explored in multiple spin systems and we derive analytical forms for polarization transfer and double quantum excitation relevant for uniformly labeled systems. Finally, the wide applicability of the fivefold sequence is demonstrated with INADEQUATE type spectra of uniformly C13 labeled sucrose and L-alanine.
Subwavelength photonic crystal waveguide in optical systems (2023)

An optical system is disclosed. The optical system comprising: a substrate; and a subwavelength photonic crystal waveguide atop the substrate, wherein the subwavelength photonic crystal waveguide comprises a periodic one or two-dimensional array of two or more interleaved dielectric pillars; wherein the periodicity of the one or two-dimensional array is constant, a combination of two or more periods, or random; wherein the one or two-dimensional array is substantially linear or curved; wherein each of the pillars of the one or two-dimensional array is at least one of a triangular prism, a trapezoidal prism, an elliptic cylinder, a cylinder, a tube, a frustum, a pyramid, a trapezoidal prism, and an asymmetric frustum; and wherein each of the pillars of the one or two-dimensional array comprises a solid, liquid, and/or gas. Other embodiments are described and claimed.
Transplantation of Thymus Tissue in Complete DiGeorge Syndrome (1999)

In some infants with profound immunodeficiency and complete DiGeorge syndrome, the transplantation of thymus tissue can restore normal immune function. Early thymus transplantation - before the development of infectious complications - may promote successful immune reconstitution.
Effect of dietary protein and estradiol-17β on growth and insulin-like growth factor I in cattle during realimentation (1995)

Forty-eight medium-framed, crossbred steers (average BW = 268 +/- 20 kg) were limit-fed a 35% concentrate diet to gain approximately .10 kg/d during a 66-d restriction (REST) period. This was followed by a 98-d realimentation (REAL) period in which steers were allotted to a 3 x 2 factorial arrangement of treatments. Treatments were 80% concentrate diets containing 9, 12, or 15% CP, and implantation of one-half of the steers with 24 mg/steer of estradiol-17 beta (E2; Compudose). The allotted steers were distributed across four pens (12 steers/pen) with each pen containing two replicates of each treatment combination. Individual feed intakes were monitored using a Calan gate system. Each steer had ad libitum access to its respective diet. Longissimus muscle area and fat thickness at the 12th rib were measured using real-time ultrasound. Dry matter intake was not affected by CP or E2 through d 56. Steers fed 9% CP weighed less (quadratic, P < .05) after d 14 than steers fed 12 or 15% CP due to slower (quadratic, P < .05) gains during this initial period. Implantation increased (P < .05) ADG from d 15 to 56 resulting in heavier BW (P < .05) on d 56 and 98. Increasing concentrations of dietary CP resulted in linear (P < .05) increases in longissimus muscle area on d 28 and 56, and fat thickness on d 98. Serum IGF-I concentrations were lowest on d -21 of REST and highest on d 28 of REAL (quadratic, P < .05).(ABSTRACT TRUNCATED AT 250 WORDS)
Association of Aurora kinase A and epidermal growth factor receptor (EGFR) gene copy number with overall survival in KRAS wild-type patients with metastatic colorectal cancer. (2010)

e14056 Background: Aurora kinase A (AURKA) regulates cell cycle progression and is under investigation as a therapeutic target. Increased AURKA gene copy number (AURKA-CN) is common in metastatic colorectal cancer (mCRC) but its relationship with the RAS pathway and clinical outcome is unknown. Increased EGFR gene copy number (EGFR-CN) in mCRC is independent of KRAS mutation status with unknown correlation with AURKA. We evaluated the frequency of high AURKA-CN in mCRC patients and correlated this finding with KRAS mutation status, EGFR-CN, and clinical outcome. Methods: We analyzed tumor DNA samples from 61 mCRC patients for KRAS mutation status and AURKA-CN, and 45 samples for EGFR-CN. Treatment information was available for 53 patients. AURKA-CN and EGFR-CN were determined by quantitative genomic PCR (“high” > 4.0 copies/cell; normal < 4.0 copies/cell). KRAS mutations were identified by direct sequencing of codons 12 and 13 of the gene. Kaplan-Meier Curve and log-rank statistics were used to estimate and compare the median survival between the groups. Hazard ratios were estimated from Cox proportional hazard method. Results: High AURKA-CN and KRAS mutation were found in 48% and 30% of samples respectively without any correlation between the two (p = 0.381). High EGFR-CN was found in 38% of samples and correlated with high AURKA-CN (p = 0.02). No significant difference in overall survival (OS) was seen between high and normal AURKA-CN (HR = 0.53, p = 0.14), yet among KRAS wild type patients high AURKA-CN was associated with improved OS (HR = 0.26, p = 0.04). Improved OS was also seen among patients with high EGFR-CN compared to normal EGFR-CN (HR-0.14, p = 0.02). Among patients receiving first or second-line chemotherapy, no difference in progression-free survival was noted between high and normal AURKA-CN patients. Conclusions: Our data demonstrate a high frequency of increased AURKA-CN which correlates with increased EGFR-CN. High AURKA-CN is associated with improved survival in KRAS wild type tumors. Further study of AURKA-CN in larger groups of homogenously treated patients with mCRC is warranted. Author Disclosure Employment or Leadership Position Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Amgen, AstraZeneca, Genentech, Genomic Health, Helsinn Group, Saladax, sanofi-aventis Saladax Amgen
Urgent Cerebral Revascularization Bypass Surgery for Iatrogenic Skull Base Internal Carotid Artery Injury (2014)

Iatrogenic injury of the skull base ICA is uncommon but can lead to lethal consequences. Many injuries can be treated with endovascular techniques. However, certain cases may still require a cerebral revascularization procedure.
An optical study of thermal convection in a passive solar heated room (1980)

Natural convection patterns associated with thermal energy storage in a passive solar heated room of the Trombe wall type were simulated with a small scale model and measured optically. The model was dynamically scaled with respect to key fluid mechanical properties. Color schlieren optics were used to obtain quantitative temperature data. Measurements from these schlieren images yielded results comparable to data generated by full-sized test facilities. Tests using this model show that hot air rising along the Trombe wall collects and remains near the ceiling, resulting in thermal stratification of the room air. Higher levels of thermal storage result in higher Trombe wall temperatures and greater differences between ceiling and floor temperatures. The study shows that vertical temperature gradients are independent of the width of the airgap between the Trombe wall and its glazing. Properly applied, the combination of reduced size room models and color schlieren optics has been demonstrated to be a useful and relatively inexpensive research tool for evaluating convective heating from thermal storage devices.
Prospective ECG-gated mouse cardiac imaging with a 34-MHz annular array transducer (2009)

Prospective imaging with electrocardiogram (ECG) and respiratory gating presents an imaging application that leverages the improved image quality of high-frequency (>20 MHz) annular arrays without the need for rapid mechanical motion. The limitation of prospective imaging is that the object being imaged must have a periodically stable motion. The present study investigated the implementation of prospective imaging with a 34 MHz annular-array scan system to image the mouse heart at high effective frame rates, >200 frames/s (fps). M-mode data for all transmit-to-receive pairs were acquired at a series of spatial locations using ECG and respiratory gating, and the data were then synthetically focused in postprocessing. The pulse-repetition frequency of the M-mode data determined the effective frame rate of the final B-mode image sequence. The hearts of adult mice were prospectively imaged and compared with retrospective data acquired with a commercial ultrasonic biomicroscope (UBM). The annular array data were acquired at an effective frame rate of 500 fps spanning 0.5 s, and the UBM data were acquired at 1000 fps spanning 0.15 s. The resulting images showed that multiple heart cycles could be clearly resolved using prospective imaging and that synthetic focusing improved image resolution and SNR of the right ventricle, interventricular septum, posterior edge of the left ventricle (LV), and papillary muscles of the LV versus fixed-focused imaging and the retrospective imaging of the UBM machine.
Neurogrid: A Mixed-Analog-Digital Multichip System for Large-Scale Neural Simulations (2014)

In this paper, we describe the design of Neurogrid, a neuromorphic system for simulating large-scale neural models in real time. Neuromorphic systems realize the function of biological neural systems by emulating their structure. Designers of such systems face three major design choices: 1) whether to emulate the four neural elements-axonal arbor, synapse, dendritic tree, and soma-with dedicated or shared electronic circuits; 2) whether to implement these electronic circuits in an analog or digital manner; and 3) whether to interconnect arrays of these silicon neurons with a mesh or a tree network. The choices we made were: 1) we emulated all neural elements except the soma with shared electronic circuits; this choice maximized the number of synaptic connections; 2) we realized all electronic circuits except those for axonal arbors in an analog manner; this choice maximized energy efficiency; and 3) we interconnected neural arrays in a tree network; this choice maximized throughput. These three choices made it possible to simulate a million neurons with billions of synaptic connections in real time-for the first time-using 16 Neurocores integrated on a board that consumes three watts.
CELL MEMBRANE DNA: A NEW TARGET FOR PSORALEN PHOTOADDUCT FORMATION (1990)

Abstract— The effects of 8‐methoxypsoralen plus long wavelength ultraviolet radiation on cell membrane DNA were examined. Treatment of human lymphocytes with 100 ng/ml 8‐methoxypsoralen and 5 J/cm 2 UVA led to the formation of 7.1 ±3.8 photoadducts per million bases. A monoclonal antibody, specific for 8‐methoxypsoralen 4′,5′4nonoadducts, was used to detect photoadducts in the cell membrane DNA of human lymphocytes and three lymphoblastoid cell lines. Treatment of lymphocytes with 8‐MOP and UVA reduced the lymphocyte DNA binding capacity by 56%. Cell membranes of normal lymphocytes were shown to contain three high affinity DNA binding proteins of 28, 59, and 79 kDa, respectively.
Precoder design for Fractional Interference Alignment (2013)

In this work, we consider a K user Interference Channel (IC), where all the transmitters employ Finite Alphabet (FA) signals. With M antennas at both transmitter and receiver nodes, the Interference Alignment (IA) scheme [1] was shown to provide 1/2 SpAC (Symbols transmitted per transmit Antenna per Channel use) per user, whereas, the Fractional Interference Alignment (FIA) scheme [2] provides a value of SpAC in the range [0,1]. When FA signals are used, the IA technique which uses a fixed value of SpAC = 1/2 is sub-optimal, and therefore will not provide the best possible rate and/or bit error rate (BER). Instead, the FIA scheme explicitly computes the maximum SpAC that can be supported for the interference channel model (assuming that accurate knowledge of the channel state information is available for the desired and the interfering signals). Hence, based on two different optimization criteria, namely (a) Coding Gain (CG) maximization, and (b) Goodput (GP) maximization, we use a simple conjugate gradient search approach to compute the sub-optimal SpAC value and the corresponding precoders for the FIA scheme. Numerical results show that for a 3 user IC, even at finite signal-to-interference ratio (SIR), (M1)/ <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">M</sub> SpAC (upper bound in FIA scheme) is achieved, as signal-to-noise ratio (SNR) tends to infinity. The BER performance is also compared between CG and GP maximization problems. Finally, the BER performance of these two optimization schemes are compared with the IA scheme, where it is shown that the proposed FIA with CG criterion outperforms the IA scheme, and will provide 0.7 dB SNR gain for the same rate.
Enhanced Capacity for Electrophoretic Capture of Plasmid DNA by Agarase Treatment of Agarose Gels (2000)

Agarase was used investigate the effect of increasing the number of polymer ends on the electrophoretic trapping of circular DNA in agarose gels. The electric field strength required to trap circular DNA was found to be the same in control and treated gels, indicating the treatment did not result in longer traps. Loading experiments indicated that treated gels had a significantly higher capacity for the open circular DNA. Electrophoretic mobility measurements using pulsed fields indicated a higher density of active traps for treated gels compared to controls. Linear dichroism experiments showed that impalement occurred by a fast and a slow process that had characteristic time constants in the one and tens of seconds ranges, respectively. The open circular DNA was more efficiently impaled in the treated gel compared to the control. The considerably higher efficiency of trapping indicated that agarase treatment increased the concentration of traps substantially.
Semi-Guiding High Aspect Ratio Core (SHARC) Fiber Laser: The Fiber Path to High Peak and Average Powers (2012)

SHARC fiber lasers offer very large rectangular core areas of 30,000 μm2 or more, peak and average powers well beyond the state of the art, good beam quality, and a mechanical flexibility allowing compact coiling.
On Perceptual Audio Compression with Side Information at the Decoder (2016)

Due to the distributed structure of many modern audio transmission setups, it is likely to have an observation at the receiver which is correlated with the desired source at the transmitter. This observation could be used as side information to reduce the transmission rate using distributed source coding. How to integrate distributed source coding into the perceptual audio compression procedure is thus a fundamental question. In this paper, we take a completely analytical approach to this problem, in particular to the rate-distortion trade-off and the corresponding coding schemes. We then interpret the results from an audio coding perspective. The main result is that, to upgrade a regular perceptual audio coder to a distributed coder, one needs to revise the perceptual masking curve. The revised masking curve models the availability of the side information as an extra masking effect, yielding lower rates. Interestingly, this means that at least conceptually, the distributed coding scenario could be integrated into the audio coder with minor changes, and without destructing the original coder.
Corrigendum to Overview of the relevance of PI3K pathway in HR-positive breast cancer (2020)

The authors regret that after publication they discovered two errors in Figure 1:1.The orange bubble “mTORC2” should read “mTORC1”. Additionally, “everolimus” and “temsirolimus” should not be indicated as inhibiting mTORC1 and mTORC2, but rather as a separate inhibition for mTORC1 only.2.“AZD6363” should be read “AZD5363”. The authors would like to apologise for any inconvenience caused. Overview of the relevance of PI3K pathway in HR-positive breast cancerAnnals of OncologyVol. 30PreviewOne of the hallmarks of hormone receptor (HR)-positive breast cancer is its dependence on the phosphatidylinositol-3-kinase (PI3K) pathway. Here, we review the epidemiologic, functional, and pharmacologic interactions between oncogenic PI3K and the estrogen receptor (ER). We discuss the epidemiology of PI3K pathway alterations, mechanisms of resistance to PI3K inhibitors, and the current mechanistic landscape of crosstalk between PI3K and ER, which provide the rationale for dual ER and PI3K inhibition and is now a standard of care in the treatment of ER+ PIK3CA-mutant metastatic breast cancer. Full-Text PDF Open Access
In Vitro Validation of Cancer Immunotherapy Reagents Using an Impedance‐Based Platform (2016)

Immunotherapy is emerging as one of the most promising approaches in cancer treatment, allowing specific targeting of cancer cells from immune cells, mediated by surface marker expression. In vitro characterization of the efficacy and potency of cancer immunotherapy reagents is a necessary step before moving to animal models and Phase I and II clinical studies. In this study we report the validation and optimization of protocols for analyzing the efficacy of reagents designed to stimulate the immune response against cancer cells using an impedance‐based and label‐free platform. The platform allows detection of cell adhesion and cell death trough monitoring the change in conductance of microelectrodes embedded in the bottom of 96‐wells cell culture plates. Because cell adhesion alters the conductivity of the electrodes, any change in cell morphology, cell adhesion or cell number is detected as variation of an impedance‐related parameter named Cell index (Ci). The platform avoids the use of any chemical label or sample processing, allowing continuous monitoring of cell activity over prolonged time periods. Furthermore, the untouched cells are still available for secondary assays that can better clarify the biological mechanism involved in the response. To mimic tumors that are target of immunotherapy efforts we utilized several carcinoma cell lines whit different level of expression of the EpCAM membrane protein. Such antigen is overexpressed in many tumors and is currently under evaluation in clinical trials. In PC3 prostate cancer cells we measured cell cytotoxicity of Primary Blood Mononuclear Cells (PBMCs) mediated by an EpCAM/CD3 Bispecific T cell Engager (BiTE) antibody. The use of the impedance‐based platform allowed measuring the full kinetic of the cytotoxic activity under different effector:target ratios and BiTE concentrations. Apoptosis of tumor cells was confirmed trough flow cytometer analysis. We also demonstrated the relation between amount of PBMCs cytotoxic activity and EpCAM surface expression trough testing MCF7 (high EpCAM expressor) and HeLa (low EpCAM expressor). To evaluate cancer immunotherapy protocols in lymphomas and leukemia, we developed a protocol where lymphomas cells are immobilized on electrodes‐coated plates and the T‐Lymphoblast cell line TALL‐104 is used as cytotoxic effector. Taken together our results demonstrate high sensitivity of the impedance‐based approach in measuring cytotoxic activity in sophisticated high throughput set up. Furthermore, the availability of continuous recording of the Cell Index over the temporal scale allows better characterization, comparing to alternative end point assays, of construct efficacy.