gebhart/patrepeval huggingface dataset:
Should evaluation for minimal residual disease be routine in acute myeloid leukemia? (2013)

MRD monitoring can help predicting the risk of relapse better than morphology and also provide endpoints for clinical testing of experimental agents. MRD can be applied to guide therapy but one must carefully consider the characteristics of the methods used and the degree of expertise of the laboratory performing the test.
A Novel Multi-Phosphonate Surface Treatment of Titanium Dental Implants: A Study in Sheep (2014)

The aim of the present study was to evaluate a new multi-phosphonate surface treatment (SurfLink®) in an unloaded sheep model. Treated implants were compared to control implants in terms of bone to implant contact (BIC), bone formation, and biomechanical stability. The study used two types of implants (rough or machined surface finish) each with either the multi-phosphonate Wet or Dry treatment or no treatment (control) for a total of six groups. Animals were sacrificed after 2, 8, and 52 weeks. No adverse events were observed at any time point. At two weeks, removal torque showed significantly higher values for the multi-phosphonate treated rough surface (+32% and +29%, Dry and Wet, respectively) compared to rough control. At 52 weeks, a significantly higher removal torque was observed for the multi-phosphonate treated machined surfaces (+37% and 23%, Dry and Wet, respectively). The multi-phosphonate treated groups showed a positive tendency for higher BIC with time and increased new-old bone ratio at eight weeks. SEM images revealed greater amounts of organic materials on the multi-phosphonate treated compared to control implants, with the bone fracture (from the torque test) appearing within the bone rather than at the bone to implant interface as it occurred for control implants.
Semiconductor approaches for tunable metamaterials in the mid-infrared (2012)

Planar metamaterials can be tailored to exhibit a wide variety of optical responses such as reflec- tion and transmission notches and highly dispersive transmission. In addition, these metamaterials can exhibit strong near-field coupling to dipole transitions located in layers placed in close prox- imity to the metallic resonators. Semiconductor heterostructures allow great flexibility for engi- neering desired dipole transitions and also allow for tuning of the transitions through the applica- tion of an electrical bias. Thus, the combination of widely tailorable metamaterial properties along with the tunablity offered by semiconductor heterostructures can provide the foundation for a new class of electrically controlled photonic devices in the mid-infrared.
Track Quality Based Multitarget Tracking Approach for Global Nearest-Neighbor Association (2012)

In multitarget tracking, in addition to the problem of measurement-to-track association, there are decision problems related to track confirmation and termination. In general, such decisions are taken based on the total number of measurement associations, length of no association sequence, and total lifetime of the track in question. For a better utilization of available information, confidence of the tracker on a particular track can be used. This quantity can be computed using the measurement-to-track association likelihoods corresponding to the particular track, target detection probability for the sensor-target geometry, and false alarm density. A track quality measure is proposed here for assignment-based global nearest neighbor (GNN) trackers. It can be noted that to compute track quality measure for assignment-based data association one needs to consider different detection events than those considered for computation of the track quality measures available in the literature, which are designed for probabilistic data association (PDA) based trackers. In addition to the proposed track quality measure, a multitarget tracker based on it is developed, which is particularly suitable in scenarios with temporarily undetectable targets. In this work, tracks are divided into three sets based on their quality and measurement association history: initial tracks, confirmed tracks, and unobservable tracks. Details of the update procedures of the three track sets are provided. The results show that discriminating tracks on the basis of their track quality can lead to longer track life while decreasing the average false track length.
Modeling perceptual grouping and figure-ground segregation by means of active reentrant connections. (1991)

The segmentation of visual scenes is a fundamental process of early vision, but the underlying neural mechanisms are still largely unknown. Theoretical considerations as well as neurophysiological findings point to the importance in such processes of temporal correlations in neuronal activity. In a previous model, we showed that reentrant signaling among rhythmically active neuronal groups can correlate responses along spatially extended contours. We now have modified and extended this model to address the problems of perceptual grouping and figure-ground segregation in vision. A novel feature is that the efficacy of the connections is allowed to change on a fast time scale. This results in active reentrant connections that amplify the correlations among neuronal groups. The responses of the model are able to link the elements corresponding to a coherent figure and to segregate them from the background or from another figure in a way that is consistent with the so-called Gestalt laws.
Open Information Extraction Using Dependency Parser for Business Rule Mining in SBVR Format (2021)

Business Rules exists at the core of any Business Organization. For efficient execution of the business system, all the business rules must be in machine-interpretable format. There is an absence of such a system that can convert the business rule sentences into corresponding structured format automatically. We present BRMiner, a system which automatically converts business rules represented as Natural Language sentences to the corresponding SBVR format which is a structured representation that can be further converted to the machine-interpretable format. BRMiner is based on the idea of Open Information Extraction (OIE). We have shown that existing OIE systems are not suitable for SBVR rule formation that leads to the development of a new OIE system BRMiner, with more accurate prediction and additional capabilities. BRMiner uses the state of the art dependency parser to convert an unstructured business rule to the corresponding structured format. We have used internal as well as publically available datasets for our system evaluation and the results are encouraging which we have shown in the paper.
Implicit discourse relation classification with syntax-aware contextualized word representations (2020)

Automatically identifying implicit discourse relations requires an in-depth semantic understanding of the text fragments involved in such relations. While early work investigated the usefulness of different classes of input features, current state-of-the-art models mostly rely on standard pre-trained word embeddings to model the arguments of a discourse relation. In this paper, we introduce a method to compute contextualized representations of words, leveraging information from the sentence dependency parse, to improve argument representation. The resulting token embeddings encode the structure of the sentence from a dependency point of view in their representations. Experimental results show that the proposed representations achieve state-of-the-art results when input to standard neural network architectures, surpassing complex models that use additional data and consider the interaction between arguments.
T cell recognition of Neisseria meningitidis class 1 outer membrane proteins. Identification of T cell epitopes with selected synthetic peptides and determination of HLA restriction elements (1991)

No vaccine is yet available against serogroup B meningococci, which are a common cause of bacterial meningitis. Some outer membrane proteins (OMP), LPS, and capsular polysaccharides have been identified as protective Ag. The amino acid sequence of the protective B cell epitopes present within the class 1 OMP has been described recently. Synthetic peptides containing OMP B cell epitopes as well as capsular polysaccharides or LPS protective B cell epitopes have to be presented to the immune system in association with T cell epitopes to achieve an optimal Ir. The use of homologous, i.e., meningococcal, T cell epitopes has many advantages. We therefore investigated recognition sites for human T cells within the meningococcal class 1 OMP. We have synthesized 16 class 1 OMP-derived peptides encompassing predicted T cell epitopes. Peptides corresponding to both surface loops and trans-membrane regions (some of which occur as amphipathic beta-sheets) of the class 1 OMP were found to be recognized by T cells. In addition, 10 of 11 peptides containing predicted amphipathic alpha-helices and four of five peptides containing T cell epitope motifs according to Rothbard and Taylor (Rothbard, J. B., and W. R. Taylor. 1988. EMBO J 7:93) were recognized by lymphocytes from one or more volunteers. Some of the T and B cell epitopes were shown to map to identical regions of the protein. At least six of the peptides that were found to contain T cell epitopes show homology to constant regions of the meningococcal class 3 OMP and the gonococcal porins PIA and PIB. Peptide-specific T cell lines and T cell clones were established to investigate peptide recognition in more detail. The use of a panel of HLA-typed APC revealed clear HLA-DR restriction patterns. It seems possible now to develop a (semi-) synthetic meningococcal vaccine with a limited number of constant T cell epitopes that cover all HLA-DR locus products.
Recent Developments In Large Area Scientific CCD Image Sensors (1989)

The design and performance of a 1024x1024 pixel charge-coupled device (CCD) imager are described. This device is fabricated utilizing a 3-phase, three-level polysilicon gate process. The chip is thinned and is employed in the back-illumination mode. Detailed measurements including imagery, read noise, full well capacity, charge transfer efficiency, linearity, dark current, spectral response, residual image, and charge collection efficiency are reported.
Strained ultrahigh performance fully depleted nMOSFETs with f/sub t/ of 330 GHz and sub-30-nm gate lengths (2006)

Ultrahigh performance fully depleted nMOSFETs have been fabricated on ultra-thin silicon-on-insulator (UTSOI) with a body thickness of 18 nm and channel lengths down to 20 nm. Uniaxial tensile stress induced in the channel using stressed contact liners and stress memorization was found to significantly improve ac performance, resulting in cutoff frequencies f/sub t/ as high as 330 GHz. This is the highest f/sub T/ value reported on fully depleted UTSOI MOSFETs and is among the highest f/sub T/ values for any Si-based field-effect transistor. Stress memorization and stressed contact liners were found to have little impact on gate to source capacitance indicating that the enhancement in f/sub T/ results primarily from stress-induced enhancements in transconductance.
Evaluation of Nasal Culturing Procedures for the Control of Atrophic Rhinitis Caused by Bordetella bronchiseptica in Swine (1977)

Control of infectious atrophic rhinitis in swine breeding herds by culturing of 3 series of nasal swab specimens from each animal, with subsequent elimination of Bordetella bronchiseptica culture-positive animals, was evaluated. Thirteen of 17 (77%) B bronchiseptica-infected herds experiencing clinical atrophic rhinitis were feedic rhinitis were freed of clinical signs of the disease by the use of this nasal culturing procedure. In 15 of 23 (65%) B bronchiseptica-infected herds, pigs were cultured negative for this organism at 4 to 10 weeks of age.
A Multiplexed Cas13-Based Assay with Point-of-Care Attributes for Simultaneous COVID-19 Diagnosis and Variant Surveillance (2022)

Point-of-care (POC) nucleic acid detection technologies are poised to aid gold-standard technologies in controlling the COVID-19 pandemic, yet shortcomings in the capability to perform critically needed complex detection-such as multiplexed detection for viral variant surveillance-may limit their widespread adoption. Herein, we developed a robust multiplexed clustered regularly interspaced short palindromic repeats (CRISPR)-based detection using LwaCas13a and PsmCas13b to simultaneously diagnose severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection and pinpoint the causative SARS-CoV-2 variant of concern (VOC)-including globally dominant VOCs Delta (B.1.617.2) and Omicron (B.1.1.529)-all the while maintaining high levels of accuracy upon the detection of multiple SARS-CoV-2 gene targets. The platform has several attributes suitable for POC use: premixed, freeze-dried reagents for easy use and storage; convenient direct-to-eye or smartphone-based readouts; and a one-pot variant of the multiplexed detection. To reduce reliance on proprietary reagents and enable sustainable use of such a technology in low- and middle-income countries, we locally produced and formulated our own recombinase polymerase amplification reaction and demonstrated its equivalent efficiency to commercial counterparts. Our tool-CRISPR-based detection for simultaneous COVID-19 diagnosis and variant surveillance that can be locally manufactured-may enable sustainable use of CRISPR diagnostics technologies for COVID-19 and other diseases in POC settings.
Fast Photoluminescence Imaging of Silicon Wafers (2006)

Photoluminescence (PL) imaging is demonstrated as a fast characterization tool allowing variations of the minority carrier lifetime within large area silicon wafers to be measured with high spatial resolution and with a data acquisition time of only one second. PL imaging is contactless and can therefore be applied to silicon solar cells before and after every processing stage including fully processed cells and bare, unpassivated mc-Si wafers, which makes it an extremely effective process monitoring tool that is ideally suited for inline applications in the PV industry. The combination of PL imaging with electroluminescence imaging and the application of PL imaging with external bias control are demonstrated to give very quick access to additional valuable information about local series resistance variations
Fuzzy Rule-Based Driver Advisory System for Fuel Economy Improvement in a Hybrid Electric Vehicle (2007)

Environmental awareness has resulted in greater emphasis on developing more environmentally friendly and fuel efficient vehicles in automotive field. Hybrid electric vehicles (HEVs) are a viable option towards achieving these goals. Ford Motor Company developed a full HEV with an e-CVT (electronically controlled continuously variable transmission), which is a power-split hybrid system power train with an integrated motor and generator. This power train exhibits great potential to improve fuel economy. Achievement of high fuel economy, however, significantly depends on the driver behavior which plays a crucial role in the full utilization of the advantages of the HEV technology. In this paper we discuss an intelligent fuzzy advisory system called the "Fuzzy Rule-Based Driver Advisory System" for Fuel Economy Improvement that automatically identifies driver's style, intentions, and preferences and provides guidance to the driver for selecting the optimal driving strategy that results in maximal fuel economy. The proposed advisory system consists of two fuzzy logic controllers (FLCs) that determine the maximal driver demand corresponding to a desired fuel economy level under current operating conditions. The output of the controller is the dynamically calculated upper bounds of the driver demand that is continually conveyed to the driver. The system serves as an automatic advisor guiding the driver to a performance that maximizes the fuel economy without significantly reducing the vehicle's speed. This Fuzzy Rule-Based Driver Advisory System for Fuel Economy Improvement was tested in a simulation environment for a Ford Escape Hybrid. Simulations results demonstrated that the proposed driver advisory system improves the overall fuel economy of the HEV by up to 3.5% without significantly compromising vehicle performance.
Synthetic Virus‐Like Particles from Self‐Assembling Coiled‐Coil Lipopeptides and Their Use in Antigen Display to the Immune System (2007)

Vanquishing viruses: Access to nanoscale particles is provided by synthetic lipopeptide building blocks that self-assemble into virus-like particles in aqueous solution, and which can be decorated with synthetic antigens for the purpose of generating humoral antigen-specific immune responses in vivo. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2007/z702805_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
Caching-aided coded multicasting with multiple random requests (2015)

The capacity of caching networks has received considerable attention in the past few years. A particularly studied setting is the shared link caching network, in which a single source with access to a file library communicates with multiple users, each having the capability to store segments (packets) of the library files, over a shared multicast link. Each user requests one file from the library according to a common demand distribution and the server sends a coded multicast message to satisfy all users at once. The problem consists of finding the smallest possible average codeword length to satisfy such requests. In this paper, we consider the generalization to the case where each user places L ≥ 1 independent requests according to the same common demand distribution. We propose an achievable scheme based on random vector (packetized) caching placement and multiple groupcast index coding, shown to be order-optimal in the asymptotic regime in which the number of packets per file B goes to infinity. We then show that the scalar (B = 1) version of the proposed scheme can still preserve order-optimality when the number of per-user requests L is large enough. Our results provide the first order-optimal characterization of the shared link caching network with multiple random requests, revealing the key effects of L on the performance of caching-aided coded multicast schemes.
Development of polymer gel barrier for containment of hazardous waste (1994)

Abstract The specific problem that is of concern here is to stop or at least significantly retard the migration of selected contaminants. Stopping or slowing migration of contaminants will allow remediation of the source of the contaminants, or at least provide more time for the required remediation technology to be developed and applied. The solution proposed is to employ a polymer gel barrier that is highly impermeable to the contaminants of interest. The barrier will be formed by injection into the ground of ungelled polymer, which will then gel in controlled fashion in situ. The importance and innovation of this proposed technique lies in ‘ungelled’. The material to be injected via drill holes will have a viscosity and density close to water, hence the pump power and costs will be very low compared with other methods. The first objective of the polymer barrier development is to identify a few potential polymers out of the hundreds possible. Two hundreds of polymers are being screened, based on established criteria. Five different polymers have been identified to form good gels. Tests have been performed to evaluate the effect of pH on the gelation time, the gel strength, and the amount of gel formed. Several cross linking agents were also studied to optimize the gel.
Molecular Layer Etching of Metalcone Films Using Lithium Organic Salts and Trimethylaluminum (2020)

Advances in semiconductor device manufacturing are limited by our ability to precisely add and remove thin layers of material in multistep fabrication processes. Recent reports on atomic layer etching (ALE) have provided the means for the precise removal of inorganic thin films deposited by atomic layer deposition (ALD), opening new avenues for nanoscale device design. Here, we report on a new technique for the precise removal of metal organic thin films deposited by molecular layer deposition (MLD), which we term molecular layer etching. This etching process employs sequential exposures of lithium organic salt (LOS) and trimethylaluminum (TMA) precursors to produce self-limiting etching behavior. We employ quartz crystal microbalance experiments to demonstrate (i) etching of alucone films preloaded with LOS upon TMA exposures and (ii) layer-by-layer etching of alucone films using alternating exposures of LOS and TMA. We also identify the selectivity of these etching mechanisms. We probe the mechanism for the layer-by-layer etching of alucone using a quartz crystal microbalance and Fourier transform infrared spectroscopy and identify that the etching proceeds via heterolytic cleaving of Al-O bonds in alucone upon LOS exposure followed by methylation to produce volatile species upon TMA exposure. The etching process results in the removal of 0.4 nm/cycle of alucone at 160 °C and up to 3.6 nm/cycle of alucone at 266 °C in ex situ etching experiments on silicon wafers. This halogen-free etching process enables etching of MLD films and provides new fabrication pathways for the control of material geometries at the nanoscale.
Data from Detecting the Presence and Progression of Premalignant Lung Lesions via Airway Gene Expression (2023)

<div>Abstract<p><b>Purpose:</b> Lung cancer is the leading cause of cancer-related death in the United States. The molecular events preceding the onset of disease are poorly understood, and no effective tools exist to identify smokers with premalignant lesions (PMLs) that will progress to invasive cancer. Prior work identified molecular alterations in the smoke-exposed airway field of injury associated with lung cancer. Here, we focus on an earlier stage in the disease process leveraging the airway field of injury to study PMLs and its utility in lung cancer chemoprevention.</p><p><b>Experimental Design:</b> Bronchial epithelial cells from normal appearing bronchial mucosa were profiled by mRNA-Seq from subjects with (<i>n</i> = 50) and without (<i>n</i> = 25) PMLs. Using surrogate variable and gene set enrichment analysis, we identified genes, pathways, and lung cancer–related gene sets differentially expressed between subjects with and without PMLs. A computational pipeline was developed to build and test a chemoprevention-relevant biomarker.</p><p><b>Results:</b> We identified 280 genes in the airway field associated with the presence of PMLs. Among the upregulated genes, oxidative phosphorylation was strongly enriched, and IHC and bioenergetics studies confirmed pathway findings in PMLs. The relationship between PMLs and squamous cell carcinomas (SCC) was also confirmed using published lung cancer datasets. The biomarker performed well predicting the presence of PMLs (AUC = 0.92, <i>n</i> = 17), and changes in the biomarker score associated with progression/stability versus regression of PMLs (AUC = 0.75, <i>n</i> = 51).</p><p><b>Conclusions:</b> Transcriptomic alterations in the airway field of smokers with PMLs reflect metabolic and early lung SCC alterations and may be leveraged to stratify smokers at high risk for PML progression and monitor outcome in chemoprevention trials. <i>Clin Cancer Res; 23(17); 5091–100. ©2017 AACR</i>.</p></div>