gebhart/patrepeval huggingface dataset:
Association between Emphysema and Chronic Obstructive Pulmonary Disease Outcomes in the COPDGene and SPIROMICS Cohorts: A Post Hoc Analysis of Two Clinical Trials (2018)

The use of thoracic computed tomographic (CT) imaging in current and former smokers is becoming increasingly more common because of its widespread availability and utility in lung cancer screening.Prior studies have demonstrated associations between CT measures of emphysema and respiratory symptoms, exacerbations, and mortality (1-5).However, thus far, practical guidance on how to incorporate increasingly available quantitative imaging data into clinical practice is lacking.In this analysis, we use data from two large NIH-sponsored cohort studies, SPIROMICS (Subpopulations and Intermediate Outcomes in COPD Study) and COPDGene (COPD Genetic Epidemiology), to examine the relationship between a readily available metric, CT-based emphysema, and risk for important patient outcomes including symptoms, exacerbations, and mortality.The goal of our analysis is not to advocate for routine CT imaging in chronic obstructive pulmonary disease (COPD) but, rather, to provide clinicians with guidance on how to translate increasingly available quantitative imaging data into information that can guide patient decision-making.We used data from COPDGene and SPIROMICS, both NIH-funded multicenter cohort studies of smokers with and without airflow obstruction.All subjects were age 40-80 years with 10 pack-years or more of exposure (6, 7).Exacerbations were defined by use of an antibiotic and/or steroid, emergency room visit, or hospital admission for a respiratory "flare-up" on the American Thoracic Society Respiratory Disease questionnaire.Exacerbation data for both cohorts were captured via longitudinal follow-up protocols.For both studies, all participants underwent spirometry before and after the administration of a short-acting bronchodilator; postbronchodilator values were used in this
Very Low Bit Rate Video Coding Based on Statistical Spatio-Temporal Prediction of Motion, Segmentation and Intensity Fields (1997)

There are a large number of applications requiring the compression of video at Very Low Bit Rates (VLBR). Such applications include wireless video conferencing, video over the internet, multimedia database retrieval and remote sensing and monitoring. Recently, the MPEG-4 standardization effort has been a motivating factor to find a solution to this challenging problem. The existing approaches to this problem can generally be grouped into block-based, model-based, and object-oriented. Block-based approaches follow the traditional strategy of decoupling the image sequence into blocks, model-based approaches rely on complex 3-D models for specific objects that are encoded, and object-oriented approaches rely on analyzing the scene into differently moving objects. All three approaches exhibit potential problems. Block-based approaches tend to generate artifacts at the boundaries of the blocks, as well as to limit the minimum achievable bit rate due to the fixed analysis structure of the scene. Model-based codecs are limited by the complex 3-D models of the objects to be encoded. On the other hand, object-oriented codecs can generate a significant overhead due to the analysis of the scene which needs to be transmitted, which in turn can be the limiting factor in achieving the target bit rates. In this chapter, we propose a hybrid object-oriented codec in which the correlations among the three information fields, e.g., motion, segmentation and intensity fields, are exploited both spatially and temporally. In the proposed method, additional intelligence is given to the decoder, resulting in a reduction of the required bandwidth. The residual information is analyzed in three different categories, i.e., occlusion, model failures, and global refinement. With other side information, it is encoded and transmitted across the channel. Experimental results are presented which demonstrate the effectiveness of the proposed approach.
Visualization of early RNA replication kinetics of SARS-CoV-2 by using single molecule RNA-FISH (2022)

SARS-CoV-2 infection continues to be a global burden. Soon after the entry, SARS-CoV-2 replicates by an elaborate process, producing genomic and subgenomic RNAs (gRNA and sgRNAs) within specialized structures called replication organelles (RO). Many questions including the timing of multiplication of gRNA and sgRNA, the generation, subcellular localization, and function of the ROs, and the mechanism of vRNA synthesis within ROs is not completely understood. Here, we have developed probes and methods to simultaneously detect the viral gRNA and a sgRNA at single cell single molecule resolution and have employed a method to scan thousands of cells to visualize the early kinetics of gRNA and sgRNA synthesis soon after the viral entry into the cell. Our results reveal that the replication is asynchronous and ROs are rapidly formed from a single RNA that enters the cell within 2 hours, which multiply to fill the entire cell cytoplasm within ~4 hours after infection. Furthermore, our studies provide a first glimpse of the gRNA and sgRNA synthesis within ROs at single molecule resolution. Our studies may facilitate the development of drugs that inhibit the virus at the earliest possible stages of replication to minimize the pathogenic impact of viral infection.
Worm Origin Identification Using Random Moonwalks (2005)

We propose a novel technique that can determine both the host responsible for originating a propagating worm attack and the set of attack flows that make up the initial stages of the attack tree via which the worm infected successive generations of victims. We argue that knowledge of both is important for combating worms: knowledge of the origin supports law enforcement, and knowledge of the causal flows that advance the attack supports diagnosis of how network defenses were breached. Our technique exploits the "wide tree" shape of a worm propagation emanating from the source by performing random "moonwalks" backward in time along paths of flows. Correlating the repeated walks reveals the initial causal flows, thereby aiding in identifying the source. Using analysis, simulation, and experiments with real world traces, we show how the technique works against both today's fast propagating worms and stealthy worms that attempt to hide their attack flows among background traffic.
Intelligent Avionics with Advanced Clustering (2008)

In this paper, we consider tracking targets using multiple distributed sensor platforms. Rather than sending the tracks to a central location, such as a command and control center where information is exchanged between platforms, we consider a distributed solution. While fixed position single sensor tracking of a single target is considered straightforward, multiple sensors on the different platforms with overlapping coverage is complex because duplicate tracking data is generated for the same targets. Redundant information generates network messages that in turn overload the network performance, and may result in traffic congestion on limited avionic bandwidth wireless links that prevents time critical data from reaching its destination. In our approach, we identify similar tracking data to be distributed and send only one copy of the message. In order to identify redundant data, we use a clustering algorithm to evaluate the large volumes of sensor information. Distributed multiple target tracking (MTT) combines track observations from different sensors to identify the same target. Massive computation and communication is required for distributed real time MTT. In this paper, the K-means clustering algorithm is used to aggregate redundant tracks. Software simulations using Matlab and emulation tests using Emulab show significant improvement of the information quality by using clustering. An MTT system was prototyped with FPGA hardware to cluster high volumes of data with low latency in real time at the network layer.
Yao’s millionaires’ problem and public-key encryption without computational assumptions (2017)

International audience
2′‐O‐[2‐[2‐(N,N‐Dimethylamino)ethoxy]ethyl] Modified Oligonucleotides: Symbiosis of Charge Interaction Factors and Stereoelectronic Effects. (2003)

Oligonucleotides with a novel, 2‘-&lt;i&gt;O&lt;/i&gt;-[2-[2-(&lt;i&gt;N,N-&lt;/i&gt;dimethylamino)ethoxy]ethyl] (2‘-&lt;i&gt;O&lt;/i&gt;-DMAEOE) modification have been synthesized. This modification,\na cationic analogue of the 2‘-&lt;i&gt;O&lt;/i&gt;-(2-methoxyethyl) (2‘-&lt;i&gt;O&lt;/i&gt;-MOE) modification, exhibits high binding affinity to target RNA (but not to DNA) and\nexceptional resistance to nuclease degradation. Analysis of the crystal structure of a self-complementary oligonucleotide containing a single\n2‘-&lt;i&gt;O&lt;/i&gt;-DMAEOE modification explains the importance of charge factors and gauche effects on the observed antisense properties. 2‘-&lt;i&gt;O&lt;/i&gt;-DMAEOE\nmodified oligonucleotides are ideal candidates for antisense drugs.
Acid Diffusion Length in Line-and-Space Resist Patterns Fabricated by Extreme Ultraviolet Lithography (2013)

Acids generated upon exposure to radiation induce the polarity change of the polymer through catalytic chain reactions in chemically amplified resists. With the reduction of feature size, the acid diffusion length increasingly becomes an important issue. In this study, we investigated the acid diffusion length in line-and-space patterns fabricated using a small field exposure tool for extreme ultraviolet (EUV) lithography and the EIDEC standard resist to clarify the acid diffusion length in a state-of-the-art resist. The acid diffusion length depended on the nominal line width and exposure dose. Upon exposure to EUV radiation with an exposure dose of 16 mJ cm -2 , the acid diffusion length (three-dimensional) in a line-and-space pattern with 21 nm nominal line width was 9.5 nm.
Ex Situ Liver Machine Perfusion: The Impact of Fresh Frozen Plasma (2019)

The primary aim of this single-center, phase 1 exploratory study was to investigate the safety, feasibility, and impact on intrahepatic hemodynamics of a fresh frozen plasma (FFP)-based perfusate in ex situ liver normothermic machine perfusion (NMP) preservation. Using an institutionally developed perfusion device, 21 livers (13 donations after brain death and 8 donations after circulatory death) were perfused for 3 hours 21 minutes to 7 hours 52 minutes and successfully transplanted. Outcomes were compared in a 1:4 ratio to historical control patients matched according to donor and recipient characteristics and preservation time. Perfused livers presented a very low resistance state with high flow during ex situ perfusion (arterial and portal flows 340 ± 150 and 890 ± 70 mL/minute/kg liver, respectively). This hemodynamic state was maintained even after reperfusion as demonstrated by higher arterial flow observed in the NMP group compared with control patients (220 ± 120 versus 160 ± 80 mL/minute/kg liver, P = 0.03). The early allograft dysfunction (EAD) rate, peak alanine aminotransferase (ALT), and peak aspartate aminotransferase (AST) levels within 7 days after transplantation were lower in the NMP group compared with the control patients (EAD 19% versus 46%, P = 0.02; peak ALT 363 ± 318 versus 1021 ± 999 U/L, P = 0.001; peak AST 1357 ± 1492 versus 2615 ± 2541 U/L, P = 0.001 of the NMP and control groups, respectively). No patient developed ischemic type biliary stricture. One patient died, and all other patients are alive and well at a follow-up of 12-35 months. No device-related adverse events were recorded. In conclusion, with this study, we showed that ex situ NMP of human livers can be performed safely and effectively using a noncommercial device and an FFP-based preservation solution. Future studies should further investigate the impact of an FFP-based perfusion solution on liver hemodynamics during ex situ normothermic machine preservation.
Quantitative correlation between promoter methylation and messenger RNA levels of the reduced folate carrier (2008)

This study further suggests that promoter methylation is a potential basis for MTX resistance. The quantitative correlation identified in this study implies that promoter methylation is possibly a mechanism involved in the fine regulation of RFC transcription.
Discovery of a novel metabotropic glutamate receptor 4 (mGlu 4) positive allosteric modulator (PAM) extended probe: Characterization of ML292, a potent and selective mGlu 4 PAM which produces efficacy alone or in combination with L-DOPA in preclinical rodent models of Parkinson's disease (2010)

ML292 was identified through a medicinal chemistry campaign that was designed to improve the in vivo characteristics of ML128 and ML182. ML292 is a potent and novel positive allosteric modulator (PAM) of the metabotropic glutamate receptor 4 (mGlu4) – hEC50 = 1196 nM; rEC50 = 330 nM. ML292 shows moderate in vitro and in vivo PK characteristics; however, ML292 was shown to be active in multiple anti-Parkinsonian animal models after systemic dosing. ML292 was superior to ML128 and ML182 in reversing haloperidol-induced catalepsy utilizing a 1.5 mg/kg dose of haloperidol. In addition, ML292 was efficacious alone or when administered in combination with L-DOPA in reversing forelimb asymmetry-induced by unilateral 6-OHDA lesions in rats. The findings that the effects of ML292 to reverse forelimb asymmetry when co-dosed with an inactive dose of L-DOPA suggests that ML292 (and other mGlu4 PAMs) may be beneficial in L-DOPA sparing activities. ML292 will find utility in the Parkinson’s and mGlu community as a novel, selective and potent PAM of mGlu4.
Mono- and Bis-Alkylation of Glyoxal-Bridged Tetraazamacrocycles Using Mechanochemistry (2015)

Glyoxal-bridged bisaminal tetraazamacrocyclic derivatives of 1,4,7,10-tetraazacyclododecane (cyclen) and 1,4,8,11-tetraazacyclotetradecane (cyclam) can be N-functionalized to incorporate coordinating groups or for conjugation to biomolecules. Herein, we present an improved N-functionalization methodology using mechanochemistry which reduces reaction times in comparison with conventional synthetic routes. A range of six alkyl halides were reacted with cyclen and cyclam bisaminal derivatives in various ratios to form mono- and bis-functionalized quaternary ammonium salts. Cross-bridged cyclam, a key intermediate for CB-TE2A, a commonly used chelator in positron emission tomography medical imaging with (64)Cu, has been synthesized using nonconventional synthetic methodologies (grinding and microwave heating) with intermediates characterized by 2D NMR and single crystal XRD. The overall synthesis time of CB-TE2A from cyclam could be shortened to 5 days from the 35 days required for the conventional synthesis.
Binding of 4-Monochlorophenol to Soil (1996)

Halogenated phenolic compounds such as chlorophenols are capable of binding to organic matter during the humification processes in soil. The incorporation of phenols into organic macromolecules, i.e., covalent bond formation, results from biologically or chemically catalyzed reactions. Standard batch sorption experiments performed in our laboratory showed a significant enhancement in soil associated 4-monochlorophenol (4-MCP) in the presence of oxygen possibly as a result of covalent binding. Sorbed 4-MCP was subjected to desorption by consecutive water and solvent extractions. Nearly 15% of the soil-associated 4-MCP remained unextracted. The unextracted [U-ring-14C]-4-MCP consisted of a fraction incorporated into humic and fulvic acids and a second fraction associated with humin or soil mineral surface and recovered as 14CO2 during soil combustion. Autoclaving the soil before 4-MCP addition resulted in a reduction in the amount of the nonextractable 14C. The addition of H2O2 caused a 4.4-fold increase in 4-MCP binding. Hydrogen peroxide, which appears to enhance both biological and abiotic coupling processes, can be added to soil as a stimulant of oxidative coupling activity.
Improving treatment geometries in total skin electron therapy: Experimental investigation of linac angles and floor scatter dose contributions using Cherenkov imaging (2018)

An updated Cherenkov imaging method identified asymmetric, machine-dependent TSET field angle pairs that provided much larger 90% isodose areas than the commonly adopted symmetric geometry suggested by Task Group 30 Report 23. A novel demonstration of scatter dose Cherenkov imaging in the TSET field was established.
Path Diversity over Packet Switched Networks: Performance Analysis and Rate Allocation (2008)

Path diversity works by setting up multiple parallel connections between the end points using the topological path redundancy of the network. In this paper, \textit{Forward Error Correction} (FEC) is applied across multiple independent paths to enhance the end-to-end reliability. Network paths are modeled as erasure Gilbert-Elliot channels. It is known that over any erasure channel, \textit{Maximum Distance Separable} (MDS) codes achieve the minimum probability of irrecoverable loss among all block codes of the same size. Based on the adopted model for the error behavior, we prove that the probability of irrecoverable loss for MDS codes decays exponentially for an asymptotically large number of paths. Then, optimal rate allocation problem is solved for the asymptotic case where the number of paths is large. Moreover, it is shown that in such asymptotically optimal rate allocation, each path is assigned a positive rate \textit{iff} its quality is above a certain threshold. The quality of a path is defined as the percentage of the time it spends in the bad state. Finally, using dynamic programming, a heuristic suboptimal algorithm with polynomial runtime is proposed for rate allocation over a finite number of paths. This algorithm converges to the asymptotically optimal rate allocation when the number of paths is large. The simulation results show that the proposed algorithm approximates the optimal rate allocation (found by exhaustive search) very closely for practical number of paths, and provides significant performance improvement compared to the alternative schemes of rate allocation.
Doubly Curved Reflector Antenna Design Trade-Offs for a Hexagonal Lattice of Beams (2021)

In this paper, a doubly curved reflector antenna fed by a stack of linear arrays is discussed. The design procedure to generate a hexagonal lattice of beams leads to higher spillover losses, resulting in lower aperture efficiency. The impact of oversizing the reflector to reduce spill-over losses is investigated with numerical results reported in Ka-band.
Coexpression of Hepatocyte Growth Factor and Its Receptor (c-met Oncogene) in HGL4 Glioblastoma Cells (1996)

Many recent studies have shown that hepatocyte growth factor (HGF) is pleiotropic. Indeed, HGF has been reported to act as a mitogen and a morphogen as well as a mitogen. To evaluate the biological significance of HGF in many cell types of different origin, we tested 32 cell lines for expression of HGF mRNA. Of 32 cell lines, 6 lines expressed HGF mRNA. Two glioblastoma cell lines, HGL4 and U138, also expressed its specific receptor (c-met oncogene) mRNA. The conditioned media of HGL4 contained 3.7-fold higher HGF activity compared to FaONeO cells as a negative control. Recombinant HGF stimulated DNA synthesis of HGL4 cells in a dose-dependent manner. In addition, anti-HGF antibody inhibited DNA synthesis of these cells. These findings suggest that coexpression of HGF and c-met oncogene stimulates growth of HGL4 glioblastoma cells.
Time-Domain Characterization of Photonic Integrated Filters Subject to Fabrication Variations (2019)

Fabrication variations are a key factor to degrade the performance of photonic integrated circuits (PICs), and especially wavelength filters. We propose an efficient modeling approach to quantify the effects of fabrication variations on the time-domain performance of linear passive photonic integrated circuits (including the wavelength filters) in the design stage, before fabrication. In particular, this novel approach conjugates the accuracy of the Polynomial Chaos (PC) expansion in describing stochastic variations and the efficiency of a Vector Fitting (VF)-based baseband modeling technique in performing time-domain simulations. A suitable example validates the performance of the proposed method.
Immobilization and activation of vanadium(III) and titanium(III) single‐site catalysts for ethylene polymerization using MgCl2‐based supports (2005)

Abstract Significant increases in the activity of vanadium(III) amidinate catalysts for ethylene polymerization have been obtained by immobilization on a MgCl 2 ‐based support prepared by reaction of AlEt 3 with a MgCl 2 /ethanol adduct. Catalyst immobilization and activation on this type of support prevents the rapid decay in activity observed under homogeneous polymerization conditions with unsupported catalysts. Stable polymerization activity is also observed with analogous titanium(III) complexes. Polyethylene with narrow molecular weight distribution and spherical particle morphology is obtained without reactor fouling. Copyright © 2005 Society of Chemical Industry
Enhanced device performances of a new inverted top-emitting OLEDs with relatively thick Ag electrode (2018)

To improve the device performances of top-emitting organic light emitting diodes (TEOLEDs), we developed a new inverted TEOLEDs structure with silver (Ag) metal as a semi-transparent top electrode. Especially, we found that the use of relatively thick Ag electrode without using any carrier injection layer is beneficial to realize highly efficient device performances. Also, we could insert very thick overlying hole transport layer (HTL) on the emitting layer (EML) which could be very helpful to suppress the surface plasmon polariton (SPP) coupling if it is applied to the common bottom-emission OLEDs (BEOLEDs). As a result, we could realize noteworthy high current efficiency of approximately ~188.1 cd/A in our new inverted TEOLEDs with 25 nm thick Ag electrode.
Fractional re-distribution among cell motility states during ageing (2020)

ABSTRACT Ageing in humans is associated with a decreased capacity to regulate cell physiology. Cellular properties, such as cell morphology and cell mechanics, encode ageing information and as a result can be used as robust ageing biomarkers. Using a panel of dermal fibroblasts derived from healthy donors spanning a wide age range, we observe an age-related reduction in average cell motility, which we show is not due to the decreased motility of all cells, but results from fractional re-distribution among motility states. By taking advantage of the single-cell nature of our motility data, we show that cells can be classified based on spatial and activity patterns that define age-dependent motility states. These findings highlight an important feature of ageing cells shown by the decrease in the heterogeneity of cell movement in older adults, that potentially offer new mechanistic insights into the ageing process and avenues for novel biomarker development.