gebhart/patrepeval huggingface dataset:
A preliminary study of acoustic propagation in thick foam tissue scaffolds composed of poly(lactic-co-glycolic acid) (2011)

The exclusive ability of acoustic waves to probe the structural, mechanical and fluidic properties of foams may offer novel approaches to characterise the porous scaffolds employed in tissue engineering. Motivated by this we conduct a preliminary investigation into the acoustic properties of a typical biopolymer and the feasibility of acoustic propagation within a foam scaffold thereof. Focussing on poly(lactic-co-glycolic acid), we use a pulse-echo method to determine the longitudinal speed of sound, whose temperature-dependence reveals the glass transition of the polymer. Finally, we demonstrate the first topographic and tomographic acoustic images of polymer foam tissue scaffolds.
Microflow cytometer (2009)

A multi-analyte diagnostic system based on a novel microflow cytometer is under development as a portable, fielddeployable sensor for environmental monitoring and for rapid point-of-care and on-site diagnosis of exposure to biothreat agents. The technology relies on a unique method for ensheathing a sample stream in continuous flow past an illuminated interrogation region. This sheathing approach efficiently focuses particles in the interrogation region of the fluidic channel and minimizes clogging by complex samples. Fluorescently coded microspheres provide the capability for highly multiplexed assays. In this report, separation of six microsphere sets was demonstrated with determination of immunoassays on three of the six sets; comparison to the commercial platform was made.
Comprehensive RNA-Seq Expression Analysis of Sensory Ganglia with a Focus on Ion Channels and GPCRs in Trigeminal Ganglia (2013)

The specific functions of sensory systems depend on the tissue-specific expression of genes that code for molecular sensor proteins that are necessary for stimulus detection and membrane signaling. Using the Next Generation Sequencing technique (RNA-Seq), we analyzed the complete transcriptome of the trigeminal ganglia (TG) and dorsal root ganglia (DRG) of adult mice. Focusing on genes with an expression level higher than 1 FPKM (fragments per kilobase of transcript per million mapped reads), we detected the expression of 12984 genes in the TG and 13195 in the DRG. To analyze the specific gene expression patterns of the peripheral neuronal tissues, we compared their gene expression profiles with that of the liver, brain, olfactory epithelium, and skeletal muscle. The transcriptome data of the TG and DRG were scanned for virtually all known G-protein-coupled receptors (GPCRs) as well as for ion channels. The expression profile was ranked with regard to the level and specificity for the TG. In total, we detected 106 non-olfactory GPCRs and 33 ion channels that had not been previously described as expressed in the TG. To validate the RNA-Seq data, in situ hybridization experiments were performed for several of the newly detected transcripts. To identify differences in expression profiles between the sensory ganglia, the RNA-Seq data of the TG and DRG were compared. Among the differentially expressed genes (> 1 FPKM), 65 and 117 were expressed at least 10-fold higher in the TG and DRG, respectively. Our transcriptome analysis allows a comprehensive overview of all ion channels and G protein-coupled receptors that are expressed in trigeminal ganglia and provides additional approaches for the investigation of trigeminal sensing as well as for the physiological and pathophysiological mechanisms of pain.
Recruitment of effector lymphocytes by initiator lymphocytes. Recruited lymphocytes are immunospecific and include graft-versus-host-reactive lymphocytes. (1976)

We have shown previously that initiator T lymphocytes (ITL), sensitized in vitro against fibroblast antigens, recruit effector T cells in vivo. After injection into hind footpads of syngeneic recipients, sensitized ITL migrated to the draining popliteal lymph nodes (PLN) and activated a trapping mechanism by which circulating lymphocytes were recruited in the PLN. This paper reports experiments designed to test the immunospecificity of these recruited T lymphocytes (RTL). We found that immunospecific RTL were depleted from other lymphoid organs during recruitment in the PLN. However, immunospecific ITL were not depleted from spleens during PLN recruitment. Thus ITL and RTL are functionally distinguishable. We show that specific GVH reactive lymphocytes were also lost from spleens and distal lymph nodes during trapping of RTL in the PLN. Thus, the trapping phase of the recruitment response is immunospecific, as are the sensitization and effector phases. The trapped RTL are antigen-specific, and include the pool of GVH-reactive-lymphocytes committed to the same alloantigen. Thus, it appears that GVH-reactive cells respond to syngeneic ITL sensitized against allogeneic fibroblasts.
Analyses of spacecraft polymeric materials (1986)

Covers advancements in spacecraft and tactical and strategic missile systems, including subsystem design and application, mission design and analysis, materials and structures, developments in space sciences, space processing and manufacturing, space operations, and applications of space technologies to other fields.
Nanostructured hydrogel based on small diameter native chitin nanofibers : Preparation, structure and properties (2014)

Nanostructured hydrogel based on small diameter native chitin nanofibers : Preparation, structure and properties
Proton Transport Chains in Glucose Metabolism: Mind the Proton (2018)

The Embden-Meyerhof-Parnas (EMP) pathway comprises eleven cytosolic enzymes interacting to metabolize glucose to lactic acid [CH<sub>3</sub>CH(OH)COO<b>H</b>]. Glycolysis is largely considered as the conversion of glucose to pyruvate (CH<sub>3</sub>COCOO<sup>-</sup>). We consider glycolysis to be a cellular process and as such, transporters mediating glucose uptake and lactic acid release and enable the flow of metabolites through the cell, must be considered as part of the EMP pathway. In this review, we consider the flow of metabolites to be coupled to a flow of energy that is irreversible and sufficient to form ordered structures. This latter principle is highlighted by discussing that lactate dehydrogenase (LDH) complexes irreversibly reduce pyruvate/H<sup>+</sup> to lactate [CH<sub>3</sub>CH(OH)COO<sup>-</sup>], or irreversibly catalyze the opposite reaction, oxidation of lactate to pyruvate/H<sup>+</sup>. However, both LDH complexes are considered to be driven by postulated proton transport chains. Metabolism of glucose to two lactic acids is introduced as a unidirectional, continuously flowing pathway. In an organism, cell membrane-located proton-linked monocarboxylate transporters catalyze the final step of glycolysis, the release of lactic acid. Consequently, both pyruvate and lactate are discussed as intermediate products of glycolysis and substrates of regulated crosscuts of the glycolytic flow.
Selective Oxidation of Betulin for the Preparation of Betulinic Acid, an Antitumoral Compound (2004)

Abstract This paper describes a semisynthetic approach for the preparation of betulinic acid from betulin. The main step of this synthetic approach is the selective oxidation of primary alcohol function of betulin. This reaction is accomplished with chromic oxide adsorbed on silica gel to obtain betulinal in an adequate yield. Betulinal is then almost quantitatively oxidized to betulinic acid by potassium permanganate action.
Determination of Deoxynivalenol in Wheat, Barley, Corn Meal, and Wheat-Based Products by Simultaneous Multisample Fluorescence Polarization Immunoassay Using a Portable Analyzer (2021)

With globalization, importing and exporting of agricultural products and foods have expanded, and food safety has become an important issue worldwide. Mycotoxin contamination of agricultural products and foods (processed foods) can occur anywhere, and it is desirable to develop a technology that can detect mycotoxin levels easily and quickly. By using a portable analyzer that can measure multiple samples simultaneously by combining a microfluidic device and a fluorescence polarization measurement system (a portable FP analyzer), we have successfully measured deoxynivalenol (DON), which is a common mycotoxin, easily and quickly by fluorescence polarized immunoassay (FPIA). The recovery rates of DON spiked in wheat, barley, cornmeal, flour, bread, pasta, thick wheat noodles (udon), and thin wheat noodles (somen) were between 86.3 and 113.2%, and the coefficient of variation was less than 8.5%. These FPIA results were in good agreement with results obtained by the official government-recognized method of liquid chromatography–mass spectrometry for DON analysis. The FP portable analyzer has great potential as an analytical tool that contributes to food safety.
Wavelength tuning of an antenna-coupled infrared microbolometer (2004)

Wavelength tuning is demonstrated in an antenna-coupled infrared microbolometer. With a 300-mV control voltage, we observed a tuning range of 0.15 μm near 10 μm. A metal-oxide-semiconductor capacitor underneath the antenna arms causes the shift of resonance wavelength with applied voltage. We develop a device model that agrees with measured results.
Comparison of Dual Retard VCT to Continuously Variable Event Valvetrain (2004)

&lt;div class="htmlview paragraph"&gt;Variable cam timing strategies which utilize retard of the intake and exhaust valve events at part load have been previously shown to provide improved fuel consumption and feedgas NOx. These benefits can be increased by enhancing the combustion system with variable charge motion.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;A variable event duration valvetrain was simulated on engine dynamometer by running a series of short duration/low lift intake valve events. The fuel consumption benefit for this simulated variable event valvetrain is compared to that of dual retard VCT with variable charge motion.&lt;/div&gt; &lt;div class="htmlview paragraph"&gt;An estimated upper limit for the fuel consumption improvement potential of variable valve timing is presented. This upper limit includes both pumping work reduction and indicated efficiency improvement with high levels of exhaust residual dilution. The measured benefits of dual retard VCT and of the variable event valvetrain are compared to the estimated upper limit.&lt;/div&gt;
SOA Models (1995)

Chapters 5 to 7 present business cycle models and their empirical application to detrended data of Germany and USA. This chapter makes the start with a very small model containing the central elements of my explanation of economic cyles. The equations of this model will appear in the same or slighty modified forms in all the models of the following chapters. The model is able to reproduce the stylized facts concerning the cyclical properties of fixed and inventory investment. It is based on the Second Order Accelerator (SOA) of investment and production. Models containing the SOA were introduced by Hillinger (Hillinger and Schüler 1977, 1978; Hillinger 1986, 1987) and further developed at SEMECON, Munich (recent contributions are Hillinger and Reiter 1992 and Reiter 1992). A microeconomic foundation of SOA models, including the derivation from an intertemporal optimization calculus and a theory of aggregation, are provided by Weser (1988, 1992) and Hillinger, Reiter and Weser (1992a). It should be noted that a very similar equation for fixed investment was used independently of Hillinger’s work by Gandolfo and Padoan (1984, 1990) as part of a model of the Italian economy. The inventory equation incorporates the production smoothing and the stock-out motive for holding inventories. It is similar to standard production smoothing models frequently used. It can also be interpreted as an SOA mechanism.
Intracavity Spectral Shaping and Chirp Tailoring from Hybrid Modelocked External Cavity Semiconductor Lasers (1999)

Compact, efficient sources of ultrashort, high repetition rate optical pulses are necessary for a variety of commercial applications. Previously, we have demonstrated the potential for shaping the intracavity modelocked spectrum of external cavity hybrid modelocked semiconductor diode lasers [1].
Hydrogel Tissue Adhesive for Sealing Corneal Incisions (2003)

The purpose of the study was to assess the efficacy of a newly developed hydrogel tissue adhesive for sealing corneal incisions in ex vivo rabbit eyes. Simple through-and-through central linear corneal incisions measuring 1-5 mm were created in enucleated rabbit eyes. As controls, the leaking pressures were measured immediately after the incisions had been made. Afterwards, the incisions were sealed with hydrogel adhesive in group 1 and with a single 10-0 nylon suture in group 2. The leaking pressure of each incision was measured after the wounds had been sealed in both groups. The leaking pressures of the controls and the sealed incisions were compared for statistical significance using the Wilcoxon signed rank test. The difference between the leaking pressures before and after sealing the incisions in groups 1 and 2 were compared using the Mann-Whitney rank sum test. The leaking pressures were significantly higher after sealing in both groups 1 and 2 compared to the controls for all incision sizes. The differences in the leaking pressures before and after adhesive application were higher than before and after suturing in all incision sizes. The differences were all statistically significant except for the 1-mm incisions. We conclude that the hydrogel glue has the potential to be used for sealing corneal incisions measuring up to 5 mm.
.alpha.-Helical versus 310-Helical Conformation of Alanine-Based Peptides in Aqueous Solution: An Electron Spin Resonance Investigation (1995)

Due to the difficulties in experimentally differentiating between the alpha- and 3(10)-helical conformations in solution, isolated helical peptides have been assumed to be in the alpha-helical conformation. However, recent electron spin resonance (ESR) studies have suggested that such peptides, in particular short alanine-based peptides, are 3(10)-helical (Miick, S. M.; et al. Nature 1992, 359, 653-5). This result prompted us to further investigate the helical conformations of alanine-based peptides in solution using electron spin resonance spectroscopy. Unlike previous investigations with a flexible link connecting the spin-label to the peptide backbone, we used a conformationally constrained spin-label (4-amino-4-carboxy-2,2,6,6-tetramethylpiperidine-1-oxyl, Toac) that is rigidly attached to the peptide backbone. From a combination of molecular modeling and ESR spectroscopy investigations, it was concluded that these alanine-based peptides exist primarily in the alpha-helical conformation, and not the 3(10)-form as previously suggested for an analogous set of peptides in aqueous environments. This discrepancy is thought to be due to the differences in flexibility of the spin-labels employed. the conformationally constrained spin-label Toac used in this study should accurately reflect the backbone conformation. Free energy surfaces, or potentials of mean force, for the conformational transition of the spin-label used in previous studies (Miick S. M.; et al. Nature 1992, 359, 653-5) suggest that this spin-label is too flexible to accurately distinguish between the alpha- and 3(10)-helical conformations.
Measurement of the longitudinal diffusion of ionization electrons in the MicroBooNE detector (2021)

Abstract: Accurate knowledge of electron transport properties is vital to understanding the information provided by liquid argon time projection chambers (LArTPCs). Ionization electron drift-lifetime, local electric field distortions caused by positive ion accumulation, and electron diffusion can all significantly impact the measured signal waveforms. This paper presents a measurement of the effective longitudinal electron diffusion coefficient, DL, in MicroBooNE at the nominal electric field strength of 273.9 V/cm. Historically, this measurement has been made in LArTPC prototype detectors. This represents the first measurement in a large-scale (85 tonne active volume) LArTPC operating in a neutrino beam. This is the largest dataset ever used for this measurement. Using a sample of ∼70,000 through-going cosmic ray muon tracks tagged with MicroBooNE's cosmic ray tagger system, we measure DL = 3.74+0.28 -0.29 cm2/s.
Editing Driver Character: Socially-Controllable Behavior Generation for Interactive Traffic Simulation (2023)

Traffic simulation plays a crucial role in evaluating and improving autonomous driving planning systems. After being deployed on public roads, autonomous vehicles need to interact with human road participants with different social preferences (e.g., selfish or courteous human drivers). To ensure that autonomous vehicles take safe and efficient maneuvers in different interactive traffic scenarios, we should be able to evaluate autonomous vehicles against reactive agents with different social characteristics in the simulation environment. We propose a socially-controllable behavior generation (SCBG) model for this purpose, which allows the users to specify the level of courtesy of the generated trajectory while ensuring realistic and human-like trajectory generation through learning from real-world driving data. Specifically, we define a novel and differentiable measure to quantify the level of courtesy of driving behavior, leveraging marginal and conditional behavior prediction models trained from real-world driving data. The proposed courtesy measure allows us to auto-label the courtesy levels of trajectories from real-world driving data and conveniently train an SCBG model generating trajectories based on the input courtesy values. We examined the SCBG model on the Waymo Open Motion Dataset (WOMD) and showed that we were able to control the SCBG model to generate realistic driving behaviors with desired courtesy levels. Interestingly, we found that the SCBG model was able to identify different motion patterns of courteous behaviors according to the scenarios.
Large-scale genomic rearrangements boost SCRaMbLE in Saccharomyces cerevisiae (2023)

Summary Genomic rearrangements contribute to gene copy number alterations, disruption of protein-coding sequences and/or perturbation of cis-regulatory networks. SCRaMbLE, a Cre/loxP-based system implanted in synthetic yeast chromosomes, can effectively introduce genomic rearrangements, and is thus a potential tool to study genomic rearrangements. However, the potential of SCRaMbLE to study genomic rearrangements is currently hindered, because a strain containing all 16 synthetic chromosomes is not yet available. Here, we constructed a yeast strain, SparLox83, containing 83 loxPsym sites distributed across all 16 chromosomes, with at least two sites per chromosome. Inducing Cre recombinase expression in SparLox83 produced versatile genome-wide genomic rearrangements, including inter-chromosomal events. Moreover, SCRaMbLE of the hetero-diploid strains derived from crossing SparLox83 with strains possessing synthetic chromosome III (synIII) from the Sc2.0 project led to increased diversity of genomic rearrangements and relatively faster evolution of traits compared to a strain with only synIII. Analysis of these evolved strains demonstrates that genomic rearrangements can perturb the transcriptome and 3D genome structure and can consequently impact phenotypes. In summary, a genome with sparsely distributed loxPsym sites can serve as a powerful tool to study the consequence of genomic rearrangements and help accelerate strain engineering in Saccharomyces cerevisiae.
Transgenic pig carrying green fluorescent proteasomes (2013)

Among its many functions, the ubiquitin-proteasome system regulates substrate-specific proteolysis during the cell cycle, apoptosis, and fertilization and in pathologies such as Alzheimer's disease, cancer, and liver cirrhosis. Proteasomes are present in human and boar spermatozoa, but little is known about the interactions of proteasomal subunits with other sperm proteins or structures. We have created a transgenic boar with green fluorescent protein (GFP) tagged 20S proteasomal core subunit α-type 1 (PSMA1-GFP), hypothesizing that the PSMA1-GFP fusion protein will be incorporated into functional sperm proteasomes. Using direct epifluorescence imaging and indirect immunofluorescence detection, we have confirmed the presence of PSMA1-GFP in the sperm acrosome. Western blotting revealed a protein band corresponding to the predicted mass of PSMA1-GFP fusion protein (57 kDa) in transgenic spermatozoa. Transgenic boar fertility was confirmed by in vitro fertilization, resulting in transgenic blastocysts, and by mating, resulting in healthy transgenic offspring. Immunoprecipitation and proteomic analysis revealed that PSMA1-GFP copurifies with several acrosomal membrane-associated proteins (e.g., lactadherin/milk fat globule E8 and spermadhesin alanine-tryptophan-asparagine). The interaction of MFGE8 with PSMA1-GFP was confirmed through cross-immunoprecipitation. The identified proteasome-interacting proteins may regulate sperm proteasomal activity during fertilization or may be the substrates of proteasomal proteolysis during fertilization. Proteomic analysis also confirmed the interaction/coimmunoprecipitation of PSMA1-GFP with 13/14 proteasomal core subunits. These results demonstrate that the PSMA1-GFP was incorporated in the assembled sperm proteasomes. This mammal carrying green fluorescent proteasomes will be useful for studies of fertilization and wherever the ubiquitin-proteasome system plays a role in cellular function or pathology.
Design of Accurate Low-Cost On-Chip Structures for Protecting Integrated Circuits Against Recycling (2015)

The recycling of electronic components has become a major industrial and governmental concern, as it could potentially impact the security and reliability of a wide variety of electronic systems. It is extremely challenging to detect a recycled integrated circuit (IC) that is already used for a very short period of time because the process variations outpace the degradation caused by aging, especially in lower technology nodes. In this paper, we propose a suite of solutions, based on lightweight negative bias temperature instability (NBTI)-aware ring oscillators (ROs), for combating die and IC recycling (CDIR) when ICs are used for a very short duration. The proposed solutions are implemented in the 90-nm technology node. The simulation results demonstrate that our newly proposed NBTI-aware multiple pair RO-based CDIRs can detect ICs used only for a few hours.
Making effective use of CASE tools in automotive systems development (1994)

CASE tools hold the key to a number of important aspects of system development. Automotive systems have reached a point in their development that demands a mature analysis and design approach. The authors describe how CASE tools offer the opportunity of communication between implementor and user and can help reduce the frequency of errors that occur in the very early stages of systems development. Hazard analysis, risk identification and containment and re-use are all potential benefits.