gebhart/patrepeval huggingface dataset:
<title>Hydrodynamic activation and sorting of white blood cells in a microfabricated lattice</title> (1997)

We demonstrate a novel hydrodynamic shear activation of leucocyte adhesion, using physiological flow conditions and a microfabricated array of channels with length scales similar to those of human capillaries. Vital chromosome stains and cell specific fluorochrome labeled antibodies reveal that the eventual adhesion of the leukocytes to the silicon array displays a strong dependence on cell type and nuclear morphology, with granulocytes activating more rapidly with distance and penetrating a smaller distance than lymphocytes. Further, the granulocytes interact with the lymphocytes in a self-exclusionary manner under shearing flow with the eventual separation of the two cell types in the array. Such arrays of microfabricated obstacles thus have an interesting potential for sorting white blood cells by type from a 10 microliter drop of whole blood.
PhosphoethanolamineN-methyltransferase (PMT-1) catalyses the first reaction of a new pathway for phosphocholine biosynthesis inCaenorhabditis elegans (2007)

The development of nematicides targeting parasitic nematodes of animals and plants requires the identification of biochemical targets not found in host organisms. Recent studies suggest that Caenorhabditis elegans synthesizes phosphocholine through the action of PEAMT (S-adenosyl-L-methionine:phosphoethanolamine N-methyltransferases) that convert phosphoethanolamine into phosphocholine. Here, we examine the function of a PEAMT from C. elegans (gene: pmt-1; protein: PMT-1). Our analysis shows that PMT-1 only catalyses the conversion of phosphoethanolamine into phospho-monomethylethanolamine, which is the first step in the PEAMT pathway. This is in contrast with the multifunctional PEAMT from plants and Plasmodium that perform multiple methylations in the pathway using a single enzyme. Initial velocity and product inhibition studies indicate that PMT-1 uses a random sequential kinetic mechanism and is feedback inhibited by phosphocholine. To examine the effect of abrogating PMT-1 activity in C. elegans, RNAi (RNA interference) experiments demonstrate that pmt-1 is required for worm growth and development and validate PMT-1 as a potential target for inhibition. Moreover, providing pathway metabolites downstream of PMT-1 reverses the RNAi phenotype of pmt-1. Because PMT-1 is not found in mammals, is only distantly related to the plant PEAMT and is conserved in multiple parasitic nematodes of humans, animals and crop plants, inhibitors targeting it may prove valuable in human and veterinary medicine and agriculture.
Binary Phase Gratings (2015)

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Design and Testing of a WR28 Waveguide Blind Mating Interconnect for mmWave ATE OTA Applications (2022)

This paper presents the design and testing of a WR28 based blind mating waveguide interconnect for over the air testing of antenna in package modules with automated test equipment. The waveguide blind mating interconnect is required for the connection between the measurement antenna that is embedded on the production test cell handler plunger and the measurement instrumentation of the automated test equipment. This interconnect needs to be disconnected each time a new device under test is inserted on the socket by the handler. This requires that the interconnect reliability is in the range of 1 million cycles or even higher for a commercial volume production test cell.
Localized surface plate modes via flexural Mie resonances (2017)

Surface-plasmon polaritons are naturally generated upon excitation of metals with high-frequency electromagnetic waves. However, the concept of spoof plasmons has made it possible to generate plasmoniclike effects in microwave electrodynamics, magnetics, and even acoustics. Similarly, in this paper, the concept of localized surface plate modes (SPMs) is introduced. It is demonstrated that SPMs can be generated on a two-dimensional (clamped or stress-free) cylindrical surface with subwavelength corrugations, which resides on a thin elastic plate, under excitation by an incident flexural plane wave. Numerical characterization of this corrugated rigid structure shows that it is elastically equivalent to a cylindrical scatterer with dispersive but uniformly negative flexural rigidity. This, indeed, suggests that plasmoniclike elastic materials can be engineered with potential applications in various areas including earthquake sensing and elastic imaging and cloaking.
Performance of high‐efficiency AMOLED displays (2001)

Abstract— In this paper, the performance of active‐matrix‐driven small‐molecule OLED displays incorporating high‐efficiency electrophosphorescent dopants were analyzed. These enable triplet excitons to contribute to light emission and have led to pixel efficiencies of over 40 lm/W. By considering a conventional two TFT per pixel addressing scheme, we show how this OLED design enables the fabrication of very‐low‐power‐consumption displays (lower than AMLCDs). We simulate display performance and perform a trade‐off analysis comparing the power consumption of displays driven by both amorphous‐silicon and low‐temperature poly‐Si TFTs.
Suitability of the electromagnetic ring expansion test to characterize materials under high strain rate deformation (2016)

Characterisation of materials under high strain rate is always challenging, and requires sophisticated apparatus. Magnetic pulse forming techniques can involve high strain rate deformation and the electromagnetic ring expansion test (ERET) is considered here to determine its suitability to characterise materials at high strain rate. The multi-physics and high speed nature of the process requires advanced numerical modelling techniques to gain insight and understanding of stress development when used as a material characterisation technique. In order to evaluate the suitability of the ERET to fully characterise the material behaviour at high strain rate, stress states were investigated using 3D coupled mechanical-electromagnetic simulations on a validated numerical model. The numerical simulations were performed in LS-Dyna® with a modified Johnson-Cook (MJC) material model in this study. Albeit the preliminary results show the development of biaxial stress during the test, a shielding mechanism is proposed to eliminate the axial component of the stress on the rings. This study indicates that the ERET has a potential to be used for characterisation of the material parameters under the influence of high strain rate.
Adaptive acoustic echo cancellation algorithms in teleconferencing systems (1989)

In teleconferencing systems, acoustic echoes consist of acoustic coupling between louder speakers and microphones and the room reverberations. The echoes could be very annoying and even cause howling if the echo level is high enough. Among many ways of canceling acoustic echoes in teleconferencing system, the adaptive digital signal processing approach is very promising since adaptive filtering has the capability to trace the change of the echo path and cancel echoes actively. Adaptive algorithms to cancel acoustic echoes in both the time and frequency domains are presented, and the computer simulation results are compared in a proposed paper. The algorithms included are LMS, NLMS, LLMS, SDLMS, SELMS, SSLMS for FIR adaptive filtering and RLMS, SHARF, and Pole-Zero for IIR adaptive filtering. Performance of these adaptation algorithms will be discussed. Subband adaptive filtering algorithm, which has a faster convergence rate, will also be presented.
Comparative genomics of Australian isolates of the wheat stem rust pathogen Puccinia graminis f. sp. tritici reveals extensive polymorphism in candidate effector genes (2015)

The wheat stem rust fungus Puccinia graminis f. sp. tritici (Pgt) is one of the most destructive pathogens of wheat. In this study, a draft genome was built for a founder Australian Pgt isolate of pathotype (pt.) 21-0 (collected in 1954) by next generation DNA sequencing. A combination of reference-based assembly using the genome of the previously sequenced American Pgt isolate CDL 75-36-700-3 (p7a) and de novo assembly were performed resulting in a 92 Mbp reference genome for Pgt isolate 21-0. Approximately 13 Mbp of de novo assembled sequence in this genome is not present in the p7a reference assembly. This novel sequence is not specific to 21-0 as it is also present in three other Pgt rust isolates of independent origin. The new reference genome was subsequently used to build a pan-genome based on five Australian Pgt isolates. Transcriptomes from germinated urediniospores and haustoria were separately assembled for pt. 21-0 and comparison of gene expression profiles showed differential expression in ∼10% of the genes each in germinated spores and haustoria. A total of 1,924 secreted proteins were predicted from the 21-0 transcriptome, of which 520 were classified as haustorial secreted proteins (HSPs). Comparison of 21-0 with two presumed clonal field derivatives of this lineage (collected in 1982 and 1984) that had evolved virulence on four additional resistance genes (Sr5, Sr11, Sr27, SrSatu) identified mutations in 25 HSP effector candidates. Some of these mutations could explain their novel virulence phenotypes.
A Fully Integrated 16-Element Phased-Array Transmitter in SiGe BiCMOS for 60-GHz Communications (2010)

A phased-array transmitter (TX) for multi-Gb/s non-line-of-sight links in the four frequency channels of the IEEE 802.15.3c standard (58.32 to 64.8 GHz) is fully integrated in a 0.12-μm SiGe BiCMOS process. It consists of an up-conversion core followed by a 1:16 power distribution tree, 16 phase-shifting front-ends, and a digital control unit. The TX core is a two-step sliding-IF up-conversion chain with frequency synthesizer that features 40 dB of gain programmability, I/Q balance and LO leakage correction, and a modulator for 802.15.3c common-mode signaling. The tradeoffs involved in the implementation of a 1:16 power distribution network are analyzed and a hybrid passive/active distribution tree architecture is introduced. Each of the 16 front-ends consists of a balanced passive phase shifter and a variable-gain, 3-stage PA that features oP <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">1dB</sub> programmability through the bias control of the its final stage. All of the chip features are digitally controllable and individual memory arrays are integrated at each front-end to enable fast beam steering through a high-speed parallel interface. The IC occupies 44 mm and is fully characterized on wafer. The TX delivers 9 to 13.5 dBm oPidB per element at 60.48 GHz with a total power consumption of 3.8 to 6.2 W. Each element attains a phase-shift range >360° with an amplitude variation <;±1 dB across phase settings and adjacent elements. Measurement results from a packaged IC in an antenna chamber are also presented including the demonstration of spatial power combining up to +40 dBm EIRP and 16-element radiation patterns.
Design and Packaging of a Vertical Free-Space Opto-electronic Interconnect System (1999)

The performance requirements of computer, telecommunication, and data-communication systems have increased considerably in recent years to the point that large-scale electronic systems are suffering from an interconnection bottleneck.
Supplementary Figures 1-6 from Enigmol: A Novel Sphingolipid Analogue with Anticancer Activity against Cancer Cell Lines and <i>In vivo</i> Models for Intestinal and Prostate Cancer (2023)

Supplementary Figures 1-6 from Enigmol: A Novel Sphingolipid Analogue with Anticancer Activity against Cancer Cell Lines and &lt;i&gt;In vivo&lt;/i&gt; Models for Intestinal and Prostate Cancer
Using automated voice calls to improve adherence to iron supplements during pregnancy (2013)

For years, researchers have explored the use of mobile phone reminders to improve adherence to medication. However, few studies have measured the direct medical benefit of those reminders, especially for low-literate populations in the developing world. This paper describes the use of automated voice calls to promote adherence to iron supplements among pregnant women in urban India. Unlike prior studies, we assess impact via a direct measurement of hemoglobin (Hb) levels in the blood. We enrolled 130 pregnant women from a low-income area of Mumbai, India and randomly assigned them to control and treatment groups. Both groups received a counseling session and a free supply of medication. The treatment group also received short audio messages, three times per week for a period of three months, encouraging them to take iron supplements. Results suggest that automated calls positively impacted Hb levels. However, because we could only recover 79 women for follow-up, and the effect size was small, our results lack statistical power (average change in Hb = 0.43 g/dL, 95% CI = -0.13 0.98 g/dL, p=0.13). We conclude that automated calls deserve further consideration for reducing maternal anemia, and we share our lessons learned for the benefit of future interventions.
Phosphorous Vacancy Nearest Neighbor Hopping Induced Instabilities in InP Capacitors: II . Computer Simulation (1988)

Drain current drift in metal insulator semiconductor devices display distinct activation energies and pre‐exponential factors. We have given evidence that these result from two physical mechanisms: thermionic tunneling of electrons into native oxide traps and phosphorous vacancy nearest neighbor hopping (PVNNH). We here present a computer simulation of the effect of the PVNNH mechanism on flatband voltage shift vs. bias stress time measurements. The simulation is based on an analysis of the kinetics of the PVNNH defect reaction sequence in which the electron concentration in the channel is related to the applied bias by a solution of the Poisson equation. The simulation demonstrates quantitatively that the temperature dependence of the flatband shift is associated with PVNNH for temperatures above room temperature.
Random, de novo and conserved proteins: How structure and disorder predictors perform differently (2023)

Abstract Understanding the emergence and structural characteristics of de novo and random proteins is crucial for unraveling protein evolution and designing novel enzymes. However, experimental determination of their structures remains challenging. Recent advancements in protein structure prediction, particularly with AlphaFold2 (AF2), have expanded our knowledge of protein structures, but their applicability to de novo and random proteins is unclear. In this study, we investigate the structural predictions and confidence scores of AF2 and protein language model (pLM)-based predictor ESMFold for de novo , random, and conserved proteins. We find that the structural predictions for de novo and random proteins differ significantly from conserved proteins. Interestingly, a positive correlation between disorder and confidence scores (pLDDT) is observed for de novo and random proteins, in contrast to the negative correlation observed for conserved proteins. Furthermore, the performance of structure predictors for de novo and random proteins is hampered by the lack of sequence identity. We also observe varying predicted disorder among different sequence length quartiles for random proteins, suggesting an influence of sequence length on disorder predictions. In conclusion, while structure predictors provide initial insights into the structural composition of de novo and random proteins, their accuracy and applicability to such proteins remain limited. Experimental determination of their structures is necessary for a comprehensive understanding. The positive correlation between disorder and pLDDT could imply a potential for conditional folding and transient binding interactions of de novo and random proteins.
Prognosis in Familial Amyotrophic Lateral Sclerosis (1997)

Familial amyotrophic lateral sclerosis (FALS) is an autosomal dominant neurodegenerative disorder affecting motor neurons and is associated with mutations in the Cu,Zn superoxide dismutase gene (SOD1) in a subset (approximately 15%) of FALS families. We analyzed 158 FALS patients from 27 families with mutations in SOD1. The mean age of onset was 45.5 +/- 8.9 years, and the mean duration of disease was 3.4 years. Forty-seven different mutations in SOD1 of FALS patients have been described worldwide. In North America, the ala4val mutation is the most common. In our patients, the ala4val mutation was associated with the most rapid progression of disease. The mean duration of disease was 1.0 +/- 0.4 years, which is significantly less than the mean duration of disease for FALS patients with mutations in SOD1 other than ala4val (p < 0.001). The duration of disease for the glu100gly mutation, 5.1 +/- 3.3 years, was significantly longer than the ala4val mutation (p < 0.001). We constructed Kaplan-Meier survival curves for the age of onset and duration of the disease for three groups of patients having mutations in SOD1: (1) ala4val; (2) glu100gly; and (3) ala4val, gly37arg, his43arg, gly85arg, gly93ala, glu100gly, leu106val, ile113thr, leu144phe, and val148gly, i.e., the entire patient population. There was no correlation between the genotype and the age of onset; 50% of affected individuals developed symptoms of ALS by the age of 47 years. As more data are collected, a more accurate prognostication of a patient's survival may be possible for specific SOD1 mutations.
Abstract 4279: Targeting Bmi1 in human prostate tumor initiating cells (2010)

Abstract Prostate cancer stem cells or tumor initiating cells (TICs) represent a barrier to effective treatment due to their intrinsic resistance to current therapeutic modalities. Recent studies identified Bmi-1 (B-cell specific MMLV insertion site-1), a member of the polycomb family of chromatin remodeling complexes, as a major oncogenic protein that is highly expressed in, and regulates stem cells and prostate TIC self-renewal. We found that shRNA specific targeting or pharmacological inhibition of the critical stem cell and TIC protein Bmi-1 in cultured prostate tumors resulted in cell death. These studies were extended to demonstrate that Bmi-1 plays an equally critical role in prostate TIC maintenance in patient tumors, and that targeting Bmi-1 eliminates the subpopulation of TICs resistant to hormone ablation and currently used chemotherapies. We utilized a novel zebrafish xenograft of primary human prostate tumor model to identify candidate Bmi-1 inhibitory drugs and other drugs targeting TIC pathways for further preclinical and clinical testing. First, we isolated and characterized TICs from fresh human prostate tissues from patients undergoing resection, and then utilized the zebrafish primary xenograft model to evaluate TIC growth, and to define Bmi-1 and other stem cell associated pathways as bonafide TIC targets. Next, we investigated Bmi-1 and other TIC inhibitors in enriched prostate stem cells and the zebrafish model, and the results were confirmed in the mouse xenograft model to determine efficacy and toxicity. Zebrafish bearing Du145 xenografts were compared to fish bearing fresh human TICs, and the combinations of Bmi-1 inhibitor(s) with taxotere, a drug approved for use in the treatment of advanced prostate cancer were synergistic. Our studies are extended to determine the features of prostate TICs in zebrafish xenograft assays, and to study the effects of Bmi-1 inhibitors in sensitized microenvironments lacking the downstream targets P16INK4a and p19Arf, in order to analyze the changes in Bmi-1 targets regulating survival, proliferation, and cancer stem cell maintenance. The novel aspects of these studies are the growth inhibition of human prostate TICs, and the use of zebrafish as an in vivo model to determine Bmi-1 inhibitor efficacy, doses and combinations with conventional therapies. Bmi-1 inhibitors that target prostate cancer TICs may provide a new class of potent inhibitors that when used alone and in combination with other targeted therapy would represent an effective therapeutic management for patients with prostate cancer. Moreover, the use of zebrafish would allow the rapid generation of response to therapy data that would facilitate the development of drugs targeted to prostate TICs. Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 101st Annual Meeting of the American Association for Cancer Research; 2010 Apr 17-21; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2010;70(8 Suppl):Abstract nr 4279.
Low-Complexity Heterogeneous Video Transcoding Using Data Mining (2008)

Recent developments have given birth to H.264/AVC: a video coding standard offering better bandwidth to video quality ratios than previous standards (such as H.263, MPEG-2, MPEG-4, etc.), due to its improved inter- and intraprediction modes at the expense of higher computation complexity. It is expected that H.264/AVC will take over the digital video market, replacing the use of previous standards in most digital video applications. This creates an important need for heterogeneous video transcoding technologies from older standards to H.264. In this paper, we focus our attention on the interframe prediction, the most computationally intensive task involved in the heterogeneous video transcoding process. This paper presents a novel macroblock (MB) mode decision algorithm for interframe prediction based on data mining techniques to be used as part of a very low complexity heterogeneous video transcoder. The proposed approach is based on the hypothesis that MB coding mode decisions in H.264 video have a correlation with the distribution of the motion compensated residual in the decoded video. We use data mining tools to exploit the correlation and derive decision trees to classify the incoming decoded MBs into one of the several coding modes in H.264. The proposed approach reduces the H.264 MB mode computation process into a decision tree lookup with very low complexity. For general validation purposes, we apply our algorithm to two of the most important heterogeneous video transcoders: MPEG-2 to H.264 and H.263 to H.264. Our results show that the our data-mining based transcoding algorithm is able to maintain a good video quality while considerably reducing the computational complexity by 72% on average when applied in MPEG-2 to H.264 transcoders, and by 62% on average when applied in H.263 to H.264 transcoders. Finally, we conduct a comparative study with some of the most prominent fast interprediction methods for H.264 presented in the literature. Our results show that the proposed data mining-based approach achieves the best results for video transcoding applications.
Synthesis of (4‐[18F]fluorophenyl)triphenylphosphonium as a potential imaging agent for mitochondrial dysfunction (2004)

Abstract Tetraphenylphosphonium (TPP) cation is able to function as a molecular probe for monitoring mitochondrial disease. The F‐18 labeled TPP, (4‐[ 18 F]fluorophenyl) triphenylphosphonium ( 18 FTPP), was therefore developed as a PET radioligand for in vivo molecular imaging of mitochondrial dysfunction. 18 FTPP was synthesized via direct nucleophilic substitution of no‐carrier‐added [ 18 F]fluoride with the precursor 4‐nitrophenyltriphenylphosphonium. After purification by HPLC, the average radiochemical yield was determined to be 10–15% and the specific activity was &gt;500 Ci/mmol at the end of synthesis. The total synthesis time was within 60 min, and the radiochemical purity of the 18 FTPP was above 95%. Copyright © 2005 John Wiley &amp; Sons, Ltd.
Wavelength switching method combined with downstream queue monitoring per ONU for &#x03BB;-tunable WDM/TDM-PON (2014)

We propose a wavelength switching method combined with queue status monitoring per ONU to improve latency of λ-switching ONU while frame loss is prevented for λ-tunable WDM/TDM-PON. Latency degradation by λ-switching of less than 4.1 ms was achieved.