gebhart/patrepeval huggingface dataset:
The Soft Compiler: A Web-Based Tool for the Design of Modular Pneumatic Circuits for Soft Robots (2022)

Developing soft circuits from individual soft logic gates poses a unique challenge: with increasing numbers of logic gates, the design and implementation of circuits lead to inefficiencies due to mathematically unoptimized circuits and wiring mistakes during assembly. It is therefore practically important to introduce design tools that support the development of soft circuits. We developed a web-based graphical user interface, <italic xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">the Soft Compiler</i> , that accepts a user-defined robot behavior as a truth table to generate a mathematically optimized circuit diagram that guides the assembly of a soft fluidic circuit. We describe the design and experimental verification of three soft circuits of increasing complexity, using the Soft Compiler as a design tool and a novel pneumatic glove as an input interface. In one example, we reduce the size of a soft circuit from the original 11 logic gates to 4 logic gates while maintaining circuit functionality. The Soft Compiler is a web-based design tool for fluidic, soft circuits and published under an open-source MIT License.
Appendix A from MTL-CEBPA, a Small Activating RNA Therapeutic Upregulating C/EBP-α, in Patients with Advanced Liver Cancer: A First-in-Human, Multicenter, Open-Label, Phase I Trial (2023)

&lt;p&gt;Trial Protocol&lt;/p&gt;
A novel 3-hydroxypropionic acid-inducible promoter regulated by the LysR-type transcriptional activator protein MmsR of Pseudomonas denitrificans (2019)

MmsR (33.3 kDa) is a putative LysR-type transcriptional activator of Pseudomonas denitrificans. With the help of 3-hydroxypropionic acid (3-HP), an important platform chemical, MmsR positively regulates the expression of mmsA, which encodes methylmalonylsemialdehyde dehydrogenase, the enzyme involved in valine degradation. In the present study, the cellular function of MmsR and its binding to the regulatory DNA sequence of mmsA expression were investigated both in vivo and in vitro. Transcription of the mmsA was enhanced >140-fold in the presence of 3-HP. In the MmsR-responsive promoter region, two operators showing dyad symmetry, designated O<sub>1</sub> and O<sub>2</sub> and centered at the -79 and -28 positions, respectively, were present upstream of the mmsA transcription start site. An electrophoretic mobility shift assay indicated that MmsR binds to both operator sites for transcription activation, probably in cooperative manner. When either O<sub>1</sub> or O<sub>2</sub> or both regions were mutated, the inducibility by the MmsR-3-HP complex was significantly reduced or completely removed, indicating that both sites are required for transcription activation. A 3-HP sensor was developed by connecting the activation of MmsR to a green fluorescent readout. A more than 50-fold induction by 25 mM 3-HP was observed.
Predicting proteome allocation, overflow metabolism, and metal requirements in a model acetogen (2019)

The unique capability of acetogens to ferment a broad range of substrates renders them ideal candidates for the biotechnological production of commodity chemicals. In particular the ability to grow with H2:CO2 or syngas (a mixture of H2/CO/CO2) makes these microorganisms ideal chassis for sustainable bioproduction. However, advanced design strategies for acetogens are currently hampered by incomplete knowledge about their physiology and our inability to accurately predict phenotypes. Here we describe the reconstruction of a novel genome-scale model of metabolism and macromolecular synthesis (ME-model) to gain new insights into the biology of the model acetogen Clostridium ljungdahlii. The model represents the first ME-model of a Gram-positive bacterium and captures all major central metabolic, amino acid, nucleotide, lipid, major cofactors, and vitamin synthesis pathways as well as pathways to synthesis RNA and protein molecules necessary to catalyze these reactions, thus significantly broadens the scope and predictability. Use of the model revealed how protein allocation and media composition influence metabolic pathways and energy conservation in acetogens and accurately predicted secretion of multiple fermentation products. Predicting overflow metabolism is of particular interest since it enables new design strategies, e.g. the formation of glycerol, a novel product for C. ljungdahlii, thus broadening the metabolic capability for this model microbe. Furthermore, prediction and experimental validation of changing secretion rates based on different metal availability opens the window into fermentation optimization and provides new knowledge about the proteome utilization and carbon flux in acetogens.
Microlens array-based exit pupil expander for full-color display applications (2004)

Retinal Scanning Display (RSD) is a near-to-eye scanned beam display technology. An exit pupil expander (EPE) or numerical aperture (NA) expander is used in RSDs to create a large display exit pupil. A novel EPE approach that uses two microlens arrays (MLA) is presented in this paper. The approach is based on cascading two identical microlens arrays spaced precisely at one focal length distance with sub-micron registration tolerances relative to each other. We demonstrated a dual MLA based EPE that: produced excellent exit pupil uniformity and better than 90% diffraction efficiency for all three wavelengths in a color display system. Registration was performed with sub-micron precision using farfield alignment techniques. Both numerical and experimental results are presented, and three fabrication technologies: grayscale lithography, photoresist reflow, and isotropic etching, are compared.
Facile “Needle‐Scratching” Method for Fast Catalyst Patterns Used for Large‐Scale Growth of Densely Aligned Single‐Walled Carbon‐Nanotube Arrays (2009)

Scratching the surface: A simple needle-scratching method (NSM) generates large-area catalyst patterns on solid substrates for the growth of densely aligned single-walled carbon-nanotube (SWCNT) arrays by chemical vapor deposition (CVD, see picture). A high density of well-aligned, ultralong SWCNTs is obtained on single-crystal quartz. This NSM could allow the fast, cheap, and large-area fabrication of CNT-based nanodevices.
CD45 Tyrosine Phosphatase Activity and Membrane Anchoring Are Required for T-Cell Antigen Receptor Signaling (1994)

T cells that lack the CD45 transmembrane tyrosine phosphatase have a variety of T-cell receptor (TCR) signaling defects that are corrected by reexpression of wild-type CD45 or its intracytoplasmic domains. In this study, a chimeric molecule containing the myristylation sequence of Src and the intracellular portion of CD45, previously shown to restore function in CD45- T cells, was mutagenized to determine if membrane-associated CD45 tyrosine phosphatase activity is required to restore TCR-mediated signaling in CD45- T cells. Abolition of enzymatic activity by substitution of a serine for a critical cysteine in the first catalytic domain resulted in failure of this molecule to restore TCR signaling. Another mutation, in which a single amino acid substitution destroyed the myristylation site, resulted in failure of the chimeric molecule to partition to the plasma membrane. Although expressed at high levels and enzymatically active, this form of intracellular CD45 also failed to restore normal signaling in CD45- T cells. These findings strongly suggest that CD45's function in TCR signaling requires its proximity to membrane-associated tyrosine phosphatase substrates.
In situ measurement of annealing-induced line shape evolution in nanoimprinted polymers using scatterometry (2009)

Thermal embossing nanoimprint lithography (NIL) is an area of continuing interest because it allows direct patterning of nanoscale structures into a wide variety of functional polymer materials. Measuring the shape evolution of nanoimprinted lines during thermal annealing can provide insights into mechanisms of polymer stability and the dynamics of polymer flow. Recently, we have used optical scatterometry to extract the profile of nanoimprinted lines in low- and high-molecular mass polymer gratings during annealing of the gratings at the glass transition temperature. The data are obtained in situ using a spectroscopic ellipsometer and analyzed using a rigorous-coupled-wave scatterometry model. The results obtained from scatterometry are in very good agreement with those measured ex situ by atomic force microscopy and specular x-ray reflectivity, revealing very different decay mechanisms for gratings in low- and high-molecular mass polymers. The role of the selection of grating model in determining the uncertainties the grating line profile extracted from scatterometry is also discussed.
CD73+ CD127high Long-Term Memory CD4 T Cells Are Highly Proliferative in Response to Recall Antigens and Are Early Targets in HIV-1 Infection (2021)

HIV-1 infection rapidly leads to a loss of the proliferative response of memory CD4+ T lymphocytes, when cultured with recall antigens. We report here that CD73 expression defines a subset of resting memory CD4+ T cells in peripheral blood, which highly express the α-chain of the IL-7 receptor (CD127), but not CD38 or Ki-67, yet are highly proliferative in response to mitogen and recall antigens, and to IL-7, in vitro. These cells also preferentially express CCR5 and produce IL-2. We reasoned that CD73+ memory CD4+ T cells decrease very early in HIV-1 infection. Indeed, CD73+ memory CD4+ T cells comprised a median of 7.5% (interquartile range: 4.5-10.4%) of CD4+ T cells in peripheral blood from healthy adults, but were decreased in primary HIV-1 infection to a median of 3.7% (IQR: 2.6-6.4%; <i>p</i> = 0.002); and in chronic HIV-1 infection to 1.9% (IQR: 1.1-3%; <i>p</i> < 0.0001), and were not restored by antiretroviral therapy. Moreover, we found that a significant proportion of CD73+ memory CD4+ T cells were skewed to a gut-homing phenotype, expressing integrins α4 and β7, CXCR3, CCR6, CD161 and CD26. Accordingly, 20% of CD4+ T cells present in gut biopsies were CD73+. In HIV+ subjects, purified CD73+ resting memory CD4+ T cells in PBMC were infected with HIV-1 DNA, determined by real-time PCR, to the same level as for purified CD73-negative CD4+ T cells, both in untreated and treated subjects. Therefore, the proliferative CD73+ subset of memory CD4+ T cells is disproportionately reduced in HIV-1 infection, but, unexpectedly, their IL-7 dependent long-term resting phenotype suggests that residual infected cells in this subset may contribute significantly to the very long-lived HIV proviral DNA reservoir in treated subjects.
Effect of a Compressive Garment on Kinematics of Jump-Landing Tasks (2016)

de Britto, MA, Lemos, AL, dos Santos, CS, Stefanyshyn, DJ, and Carpes, FP. Effect of a compressive garment on kinematics of jump-landing tasks. J Strength Cond Res 31(9): 2480-2488, 2017-During jump-landing tasks, knee kinematics such as excessive valgus have been linked to knee injury in females. We determine the influence of a compressive garment on knee valgus during landing. Physically active women (n = 27, mean age 23 years) performed 4 different jump-landing tasks with 2 apparel conditions (compressive garment and regular sports shorts). Kinematic data were collected to determine knee flexion and valgus angles and the maximum jump height. Results showed that the compressive garment decreased knee flexion and knee valgus range of motion, without significant changes in the maximum jump height. As a practical application, we suggest that compression could be a strategy to reduce dynamic valgus without influencing jump performance, which motivates further study of its potential for knee injury prevention.
An investigation of input protection for CDM robustness in 40nm CMOS technology (2009)

Abstract- Adiabatic failures due to an initial peak voltage of VF-TLP measurements were observed at the input gate of a 40nm CMOS technology. Moreover, a correlation was verified between the failure current of the VF-TLP measurements and failure voltage of CDM testing. Through the transient analyses by a VF-TLP system, the performance of a diode-stack was better than that of SCRs as an input protection for CDM robustness. I.
Generation of Mouse iNKT Cell Lines (2013)

Natural killer T (NKT) cells bridge the innate and adaptive arms of the immune system, and manipulating their effector functions can have therapeutic significances in the treatment of autoimmunity, transplant biology, infectious disease and cancer. This important lymphocyte subset regulates the immune system through their potent cytokine production following the recognition of lipid antigen present in the context of the MHC class I-like CD1d molecule, in addition their ability to directly mediate cytotoxicity. Here, we describe a method of expanding mouse invariant NKT (iNKT) cell lines from mononuclear cells isolated from the thymus, spleen, or liver using bone marrow derived dendritic cells. These iNKT cell lines can be used study their co-signaling requirements, cytokine profiles and cytotoxic functions which will greatly enhance our knowledge of iNKT cell biology.
Growth analysis of self-formed Ti-rich interface layers in Cu(Ti)/dielectric-layer samples using Rutherford Backscattering Spectrometry (2009)

The Rutherford backscattering spectrometry (RBS) technique was employed for the growth investigation of Ti-rich interface layers in the annealed Cu(Ti) dielectric-layer . Growth behavior observed in RBS was similar to that in TEM. Thus, the RBS technique is indicated to be appropriate method for the growth analysis of the Ti-rich interface layers.
Modelling of the terahertz communication channel for in-vivo nano-networks in the presence of noise (2016)

This paper focuses on the modelling of communication channel noise inside human tissues at the THz band (0.1-10THz). A novel model is put forward based on the study of the physical mechanism of the channel noise in the medium, which takes into account both the radiation of the medium and the molecular absorption from the transmitted signal. The derivation and the general concepts of the noise modelling is detailed in the paper. The results show that the channel noise power spectral density at the scale of several micrometres is at acceptable levels and the value tends to decrease with the increase of both distance and frequency. In addition, the channel noise is also related to the composition of the human tissues, with the result of higher channel noise in tissues with higher water concentration. The conclusion drawn from the conducted study and analysis paves the way for more comprehensive characterisation of the electromagnetic channel within in-vivo nano-networks.
Evaluation of an automated quantitative latex immunoturbidimetric non-treponemal assay for diagnosis and follow-up of syphilis: a prospective cohort study (2017)

<b>Purpose.</b> We evaluated the Sekure rapid plasma reagin (RPR-S) (Sekisui Diagnostics) automated quantitative latex immunoturbidimetric assay performed on the SK500 clinical chemistry system for clinical appropriateness.<b>Methodology.</b> Syphilis-infected individuals and controls were recruited into a prospective cohort study conducted at a sexually transmitted infection clinic in Antwerp, Belgium. Sera collected at diagnosis (baseline) and at 3, 6, 9 and 12 months post-treatment were tested with RPR-S and Macro-Vue RPR card (RPR-C) (Becton Dickinson) assays; RPR-C was considered the reference test. IgG/IgM enzyme immunoassay and <i>Treponema pallidum polA</i> serum PCR results were consulted by discordancy at baseline. Categorical analyses were performed and correlations were assessed with (non)-linear regression. Post-treatment longitudinal serological evolution was evaluated.<b>Results.</b> A total of 463 samples from 120 new syphilis cases from a variety of clinical stages and 30 syphilis-negative controls were tested. Initially, there was a weak correlation between quantitative RPR-C/S (<i>r</i>=0.15). In 70 samples there was a strong suspicion of hook effect. Of these, 57/70 sera were retested with an extra dilution step, resulting in an average 12-fold increase in quantitative RPR-S results. After the extra dilution, the overall qualitative RPR-C/S agreement was 78.89 %, (κ-coefficient: 0.484). Of the 92 discordant samples, 9 were from the baseline visit (RPR-C titre: 1-8), which could have led to possible missed diagnoses using the RPR-S.<b>Conclusions.</b> The sensitivity and accuracy of the RPR-S test requires improvement before it can be used to diagnose syphilis and evaluate treatment efficacy in clinical practice.
Probabilistic modeling of transaction data with applications to profiling, visualization, and prediction (2001)

Transaction data is ubiquitous in data mining applications. Examples include market basket data in retail commerce, telephone call records in telecommunications, and Web logs of individual page-requests at Web sites. Profiling consists of using historical transaction data on individuals to construct a model of each individual's behavior. Simple profiling techniques such as histograms do not generalize well from sparse transaction data. In this paper we investigate the application of probabilistic mixture models to automatically generate profiles from large volumes of transaction data. In effect, the mixture model represents each individual's behavior as a linear combination of "basis transactions." We evaluate several variations of the model on a large retail transaction data set and show that the proposed model provides improved predictive power over simpler histogram-based techniques, as well as being relatively scalable, interpretable, and flexible. In addition we point to applications in outlier detection, customer ranking, interactive visualization, and so forth. The paper concludes by comparing and relating the proposed framework to other transaction-data modeling techniques such as association rules.
Lithium Tetrafluoroborate-Based Ester Electrolyte Formulations to Improve the Operating Temperature Range in NCM 622 || Graphite Li-Ion Batteries (2023)

The use of alternative lithium salts, lithium tetrafluoroborate (LiBF4), lithium difluoro(oxalato)borate, and lithium hexafluorophosphate (LiPF6), in the ester/fluoroethylene carbonate electrolyte results in improved low-temperature performance at −20 °C compared to LiPF6 in a carbonate-based electrolyte, but the room-temperature performance of the ester-based formulation has significant capacity fade due to the instability of the solid electrolyte interphase (SEI). Incorporation of electrolyte additives, lithium bis(oxalato)borate, lithium difluorophosphate, and lithium bis(trimethylsilyl) phosphate (LiTMSP), into lithium tetrafluoroborate (LiBF4) ester-based electrolytes (methyl acetate/fluoroethylene carbonate-MA/FEC) has been investigated in graphite//LiNi0.6Co0.2Mn0.2O2 cells to improve room-temperature cycling stability without diminishing low-temperature rate performance. The LiBF4-based ester electrolyte containing 1% LiTMSP delivers the highest reversible capacity at low temperature (−20 °C), while the room-temperature performance is significantly improved compared to that of the base ester-based electrolyte (LiBF4-MA) and almost comparable to that of the standard carbonate-based electrolyte. The improved electrochemical performance for 1% LiTMSP at −20 °C is due to the lower charge transfer resistance as supported by electrochemical impedance spectroscopy, and improved room-temperature performance can be ascribed to the generation of a stable phosphate-rich SEI on the graphite surface as revealed by X-ray photoelectron spectroscopy.
Refining the CAMP Crash Alert Timing Approach by Examining "Last Second" Braking and Lane Change Maneuvers under Various Kinematic Conditions (2004)

This study is part of the Crash Avoidance Metric Partnership (CAMP)/ NHTSA Forward Collision Warning (FCW) system program, which will eventually encompass a series of four human factors studies. The present study examines drivers' last-second braking and last-second steering (or lane-change) judgments. Drivers performed last-second braking and steering maneuvers under instructions for normal or hard intensity responses under a wide variety of vehicle-to-vehicle kinematic scenarios. This strategy of varying instruction during these last-second maneuvers was taken so that driver perceptions of normal and non-normal kinematics situations (or envelopes) could be properly identified and modeled for crash alert timing purposes. In addition, unlike previous CAMP work that only examined lead vehicle stationary and lead vehicle braking scenarios, the current study also included scenarios where the lead vehicle was moving at a slower but constant speed prior to the last-second maneuver. Results provided validation of the required deceleration model developed in the prior CAMP FCW project. In addition, a new model was developed, referred to as the 3-tiered inverse time-to-collision model. This promising model assumes the driver deceleration response (in response to the crash alert) is based on an inverse time-to-collision threshold that decreases linearly with speed.
Content protection for games (2006)

In this paper we review the state of the art in content protection for video games by describing the capabilities and shortcomings of currently deployed solutions. In an attempt to address some of the open issues, we present two novel approaches. The first approach uses branch-based software watermarking to discourage and detect piracy through a registration-based system. In the second approach, based on the parallels between games and premium audio and video content, we propose the use of current physical-media copy-protection technologies for gaming content. In particular, we focus on broadcast encryption technology. The use of an open, standard-based architecture enables the development of a more restrictive protection system for games. Finally, we demonstrate how the proposed protection mechanisms can be applied to video-game copy protection through five scenarios.
An 8-Tap CMOS Lock-In Pixel Image Sensor for Short-Pulse Time-of-Flight Measurements (2020)

An 8-tap CMOS lock-in pixel image sensor that has seven carrier-capturing and a draining time window was developed for short-pulse time-of-flight (TOF) measurements. The proposed pixel for the short-pulse TOF measurements has seven consecutive time-gating windows, each of which has the width of 6 ns, which is advantageous for high-resolution range imaging, particularly for relatively longer distances (>5 m) and under high ambient light operations. In order to enhance the depth resolution, a technique for the depth-adaptive time-gating-number assignment (DATA) for the short-pulse TOF measurement is proposed. A prototype of the 8-tap CMOS lock-in pixel image sensor is implemented with a 1POLY 4METAL 0.11-μm CIS process. The maximum non-linearity error of 1.56%FS for the range of 1-6.4 m and the depth resolution of 6.4 mm was obtained at 6.2 m using the DATA technique.