gebhart/patrepeval huggingface dataset:
Thermodynamic Scale of β-Amino Acid Residue Propensities for an α-Helix-like Conformation (2018)

A thiol-thioester exchange system has been used to measure the propensities of diverse β-amino acid residues to participate in an α-helix-like conformation. These measurements depend on formation of a parallel coiled-coil tertiary structure when two peptide segments become linked by thioester formation. One peptide segment contains a "guest" site that accommodates diverse β residues and is distal to the coiled-coil interface. We find that helix propensity is influenced by side chain placement within the β residue [β<sup>3</sup> (side chain adjacent to nitrogen) slightly favored relative to β<sup>2</sup> (side chain adjacent to carbonyl)]. The previously recognized helix stabilization resulting from five-membered ring incorporation is quantified. These results are significant because so few quantitative thermodynamic measurements have been reported for α/β-peptide folding.
Learning hybrid force and position control of robot manipulators (1993)

The learning control is applied to hybrid force and position control of robot manipulators. When the geometry and position of a constraint surface is known, the hybrid force and position controller and the feedforward compensator can be designed in the constraint coordinates. When the operation is periodic, the learning hybrid force and position control enhance the control performance as the feedforward compensator is updated in each cycle by the force and position error in the preceding trials. This scheme is proved to be asymptotically stable. A two degree of freedom SCARA-type direct-drive robot manipulator is used to test the learning hybrid force and position control. The deburring tool mounted on the upper link of the robot could follow a flat, tilted flat, and curved 1/4 " aluminum plate with a desired contact force of 10 N (within the root-mean-square force error of 1.95 N) and with a desired tangential velocity. The experiments confirmed the effectiveness of the learning hybrid force and position controller.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Improving yield and reliability of FIB modifications using electrical testing (1998)

Focused Ion Beam technology has two main areas of application for ICs: modification and preparation for technological analysis. The most solicited area is modification. This involves physically modifying a circuit by cutting lines and creating new ones in order to change the electrical function of the circuit. IC planar technologies have an increasing number of metal interconnections making FIB modifications more complex and decreasing their changes of success. The yield of FIB operations on ICs reflects a downward trend that imposes a greater number of circuits to be modified in order to successfully correct a small number of them. This requires extended duration, which is not compatible with production line turn around times. To respond to this problem, two solutions can be defined: either, reducing the duration of each FIB operation or increasing the success rate of FIB modifications. Since reducing the time depends mainly on FIB operator experience, insuring a higher success rate represents a more crucial aspect as both experienced and novice operators could benefit from this improvement. In order to insure successful modifications, it is necessary to control each step of a FIB operation. To do this, we have developed a new method using in situ electrical testing which has a direct impact on the yield of FIB modifications. We will present this innovative development through a real case study of a CMOS ASIC for high-speed communications. Monitoring the electrical behavior at each step in a FIB operation makes it possible to reduce the number of circuits to be modified and consequently reduces system costs thanks to better yield control. Knowing the internal electrical behavior also gives us indications about the impact on reliability of FIB modified circuits. Finally, this approach can be applied to failure analysis and FIB operations on flip chip circuits.
A Nonenzymatic and Automated Closed-Cycle Process for the Isolation of Mesenchymal Stromal Cells in Drug Delivery Applications (2018)

The adipose tissue is a good source of mesenchymal stromal cells that requires minimally invasive isolation procedures. To ensure reproducibility, efficacy, and safety for clinical uses, these procedures have to be in compliant with good manufacturing practices. Techniques for harvesting and processing human adipose tissue have rapidly evolved in the last years, and Lipogems® represents an innovative approach to obtain microfragmented adipose tissue in a short time, without expansion and/or enzymatic treatment. The aim of this study was to assess the presence of mesenchymal stromal cells in the drain bag of the device by using a prototype Lipogems processor to wash the lipoaspirate in standardized condition. We found that, besides oil and blood residues, the drain bag contained single isolated cells easy to expand and with the typical characteristics of mesenchymal stromal cells that can be loaded with paclitaxel to use for drug-delivery application. Our findings suggest the possibility to replace the drain bag with a "cell culture chamber" obtaining a new integrated device that, without enzymatic treatment, can isolate and expand mesenchymal stromal cells in one step with high good manufacturing practices compliance. This system could be used to obtain mesenchymal stromal cells for regenerative purposes and for drug delivery.
Performance Analysis of Two Competing DADO PE Designs (1983)

In parallel processing, useful computation is performed by having a number or processors computing values and communicating these results to neighboring processors. It is a crucial design issue in any parallel processing architecture to determine the optimal balance or resources for competing requirements of typical problems to be solved by the device, i.e. computation versus communication. For example, in a highly parallel machine consisting of many individual processing elements (PE's), there is a trade ofr between the complexity of the constituent PE's and the number of such elements which may be embedded in a fixed silicon area. Part or the PE's circuitry must be dedicated to communication processing. Increasing the ability and the speed at which a PE can perform communication can be done, but only at the expense or the number of processors on a chip. DADO is a large scale VLSI computer designed for the rapid execution of AI production systems. This paper analyses the nature of the instruction stream expected to be executed on DADO for production system applications, with emphasis placed on the number or processors in the machine and the size of the problem. We describe four different proposed methods of handling I/O and their queueing network models. The models were carefully simulated to determine which I/O scheme and its resulting circuit complexity is best suited (most efficient) with respect to the DADO instruction stream.
Antigen Uptake by Dendritic Cells (2003)

Newly generated dendritic cells (DC) migrate from the bone marrow to the nonlymphoid tissues presumably through the blood stream (peripheral blood DC). During injury, tissue DC (such as Langerhans cells [LC] in the epidermis) capture antigen and then, under microenvironmental signals, leave the nonlymphoid tissues through the afferent lymph as veiled cells (see Fig. 1). During their migration, DC undergo maturation, including loss of antigen uptake and acquisition of costimulatory function. Then, DC enter into lymph nodes where they home to the T-cell rich area (inderdigitating cells) and induce an antigen specific primary T-cell response. Fig. 1. Life cycle of dendritic cells. Newly generated dendritic cells migrate, from the bone marrow to the nonlymphoid tissues presumably through the blood stream (peripheral blood DC). During an injury, tissue dendritic cells (such as LC in the epidermis) capture the antigen and then, under microenvironmental signals (such as TNFα production in the dermis) leave the nonlymphoid tissues through the afferent lymph (veiled cells). During their migration, DC undergo maturation, including loss of antigen uptake and aquisition of costimulatory function. Then, DC enter into lymph nodes where they home to the T-cell rich area (interdigitating cells) and induce an antigen specific primary T-cell response. Few DC exit lymph nodes possibly because they may either be programmed to die after antigen presentation or destroyed by the afferent immune response.
Ultra-sensitive SnO2 gas sensors based on hierarchical octahedra (2016)

The controlled hydrolysis of Sn <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">II</sup> precursor ([Sn(NMe) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ] <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) yields micrometric Sn <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3</sub> O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> (OH) <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> octahedra, formed by a self-assembly process. The water content and alkylamine surfactants are major parameters for the growth process. These structures have been employed to prepare highly sensitive gas sensors, which present 7% variation of their resistance at only 0.25 ppm CO.
Tissue Recombination Models for the Study of Epithelial Cancer (2015)

Animal models of cancer provide fundamental insight into the cellular and molecular mechanisms of human cancer development. As an alternative to genetically engineered mouse models, increasing evidence shows that tissue recombination and transplantation models represent an efficient approach to faithfully recapitulate solid epithelial cancer in mice. Cancer can be rapidly initiated through lentiviral delivery of defined genetic alterations into target cells that are grown in a physiological milieu with an appropriate epithelial-stromal interaction. Through genetic manipulation of distinct subpopulations of epithelial cells and mesenchymal cells, this powerful system can readily test both cell-autonomous roles of genetic events in the epithelial compartment and the paracrine effects of the microenvironment. Here we review the recent advances in mouse models of several epithelial cancers achieved using orthotopic transplantation and tissue recombination strategies, with an emphasis on the dissociated cell in vivo prostate regeneration model to investigate prostate cancer.
Conditions for Multi-Antenna Selection to be Optimal Given Channel Amplitude Information (2006)

Transmitter designs based on partial channel state information (CSI) have become increasingly attractive in multi-antenna wireless communication systems. To capture partial CSI statistics at the transmitter, we rely on a channel amplitude information (CAI) model, based on which we aim for maximizing the random channel's average mutual information. Due to the high computational complexity required for such optimal transmissions, we resort to reduced complexity practical schemes and derive necessary and sufficient conditions for these alternatives to achieve maximal average mutual information
Abstract 1670: Sabizabulin shows anti-cancer efficacy in HER2+ breast cancer and novel sabizabulin derivatives overcome paclitaxel-resistance in triple negative breast cancer (2023)

Abstract Of the four breast cancer molecular subtypes, the HER2 overexpressing subtype (HER2+) accounts for 15% of all breast cancer cases. Preferred frontline treatment relies on anti-HER2 therapies, such as trastuzumab and pertuzumab, combined with microtubule inhibitors, such as taxanes. However, the clinical efficacy of taxanes is limited by development of chemoresistance and hematological and neurotoxicities. Other agents that target tubulin, such as colchicine-binding site inhibitors (CBSIs) are a class of promising alternatives to taxane therapy due to their ability to overcome P-gp-mediated taxane resistance. Sabizabulin (formerly known as VERU-111) is a potent CBSI that is orally bioavailable, overcomes paclitaxel resistance, and inhibits tumor growth and distant metastases in triple negative breast cancer (TNBC). Here, we demonstrate sabizabulin’s anti-cancer efficacy in HER2+ breast cancer. We report that sabizabulin inhibits proliferation of HER2+ breast cancer, maintains a low nanomolar IC50 value, inhibits colony formation, and causes apoptosis in HER2+ breast cancer cell lines. Sabizabulin inhibits the primary tumor growth in an orthotopic HER2+ in vivo model, BT474, and in a patient-derived xenograft model, HCI-12. While sabizabulin shows promising results for treatment in HER2+ breast cancer, we further optimized the structure of sabizabulin to create a new class of anti-cancer molecules: 40a, CH-2-77, and 60c. Based on in vitro data, 60c showed higher potency in HER2+ breast cancer cell lines and was chosen as the lead compound to further study in a paclitaxel-resistant triple negative breast cancer in vivo study where it was able to effectively inhibit primary tumor growth compared to the vehicle group. Citation Format: Kelli L. Hartman, Raisa I. Krutilina, Damilola Oluwalana, Deanna N. Parke, Hao Chen, Duane D. Miller, Wei Li, Tiffany N. Seagroves. Sabizabulin shows anti-cancer efficacy in HER2+ breast cancer and novel sabizabulin derivatives overcome paclitaxel-resistance in triple negative breast cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1670.
Discovery of Highly Potent, Selective, and Brain-Penetrable Leucine-Rich Repeat Kinase 2 (LRRK2) Small Molecule Inhibitors (2012)

There is a high demand for potent, selective, and brain-penetrant small molecule inhibitors of leucine-rich repeat kinase 2 (LRRK2) to test whether inhibition of LRRK2 kinase activity is a potentially viable treatment option for Parkinson's disease patients. Herein we disclose the use of property and structure-based drug design for the optimization of highly ligand efficient aminopyrimidine lead compounds. High throughput in vivo rodent cassette pharmacokinetic studies enabled rapid validation of in vitro-in vivo correlations. Guided by this data, optimal design parameters were established. Effective incorporation of these guidelines into our molecular design process resulted in the discovery of small molecule inhibitors such as GNE-7915 (18) and 19, which possess an ideal balance of LRRK2 cellular potency, broad kinase selectivity, metabolic stability, and brain penetration across multiple species. Advancement of GNE-7915 into rodent and higher species toxicity studies enabled risk assessment for early development.
A hollow-fiber membrane bioreactor for the removal of trichloroethylene from the vapor phase (2000)

A hollow-fiber membrane bioreactor was used to separate trichloroethylene (TCE) from a gaseous waste stream with subsequent cometabolic biodegradation by a pure culture of Methylosinus trichosporium OB3b PP358. The two-stage bioreactor system was successfully operated for 20 days. PP358 was grown in a continuous-flow chemostat and circulated through the fiber lumen of a hollow-fiber membrane module (HFMM), while TCE contaminated air (141 to 191 microg/L) was pumped through the HFMM shell. Between 54% -84% TCE transfer and 92%-96% TCE cometabolism were obtained in the HFMM reactor loop. Short shell-residence times, 1.6 to 5.0 minutes, demonstrated quick throughput of TCE contaminated air. Best-fit computer modeling of the biological experiments estimated mass transfer coefficients between 2.0 x 10(-3) cm/min and 5.6 x 10(-3) cm/min. The average pseudo-first-order biodegradation rate constant for the biological experiments was 0.46 L/mg TSS/d. These results demonstrate that the hollow-fiber membrane bioreactor represents an attractive technology for the bioremediation of gaseous waste streams.
2.4 A Distributed Autonomous and Collaborative Multi-Robot System Featuring a Low-Power Robot SoC in 22nm CMOS for Integrated Battery-Powered Minibots (2019)

Multi-robot systems, working collectively to accomplish complex missions beyond the capability of a single robot, are required for a wide range of applications such as search-and-rescue, precision agriculture and industrial automation. The collective behavior of a multi-robot system is governed by its continuous interactions with the physical environment, inter-robot information exchange, and intelligent decision making. Energy-efficient performance, size, weight and scalability of the key sensor, compute, communication, control and actuator components [1-3] of the individual robot platform are critical for realizing efficient advanced systems. In this paper, we demonstrate a distributed, autonomous and collaborative multi-robot system featuring integrated, battery-powered, crawling and jumping minibots for an example search-and-rescue application. We present a 16 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> low-power Robot SoC in 22 nm CMOS that is integrated in the cm-scale minibot platform along with audiovisual and motion sensors, battery, low-power wireless communication and motion actuator components (Fig. 2.4.7).
Repeated Measures Testing of Driver Collision Warning (2015)

&lt;div class="section abstract"&gt;&lt;div class="htmlview paragraph"&gt;This paper investigates the effects on response time of a forward collision event in a repeated-measures design. Repeated-measures designs are often used in forward collision warning (FCW) testing despite concerns that the first exposure creates expectancy effects that may dilute or bias future outcomes. For this evaluation, 32 participants were divided into groups of 8 for an AA, BB, AB, BA design (A= &lt;i&gt;No Warning&lt;/i&gt;; B=&lt;i&gt;FCW&lt;/i&gt; alert). They drove in a high-fidelity simulator with a visual distraction task. After driving 15 min in a nighttime rural highway environment, a forward collision threat arose during the distraction task (Period 1). A second drive was then run and the forward collision threat was repeated again after ∼10 min (Period 2). The response times from these consecutive events were analyzed. The results indicated there was differential carryover and significant Period 1 vs. 2 effects that diluted the magnitude of difference between &lt;i&gt;FCW&lt;/i&gt; and &lt;i&gt;No Warning&lt;/i&gt; treatments relative to first exposure only. Also, there was a non-significant trend suggesting that previous trials with FCW can slow responses on later trials with no FCW. The findings suggest that driver warning HMI evaluations should exercise care in using repeated exposures to low-probability critical events. Researchers should explore carryover effects when repeated-measures designs are used, or else avoid repeated exposures to low-probability, unexpected critical events altogether.&lt;/div&gt;&lt;/div&gt;
Patients with Idiopathic Pulmonary Fibrosis with Antibodies to Heat Shock Protein 70 Have Poor Prognoses (2012)

Patients with IPF with anti-HSP70 autoantibodies have more near-term lung function deterioration and mortality. These findings suggest antigen-specific immunoassays could provide useful clinical information in individual patients with IPF and may have implications for understanding IPF progression.
MMC converter cells employing ultrahigh-voltage SiC bipolar power semiconductors (2017)

This paper investigates the benefits of using high-voltage converter cells for transmission applications. These cells employ ultrahigh-voltage SiC bipolar power semiconductors, which are optimized for low conduction losses. The Modular Multilevel Converter with half-bridge cells is used as a test case. The results indicate a reduction of converter volume and complexity, while maintaining low losses and harmonic performance.
Loss of KAI1 expression in the progression of colorectal cancer. (1999)

The transmembrane 4 superfamily member KAI1 (CD82) has been shown to inhibit pulmonary metastases in experimental metastasis models of prostate cancer and melanoma. KAI1 expression is decreased in the progression of common solid epithelial tumors of adulthood, including lung, prostate, breast, esophageal, gastric, pancreatic, and bladder cancers. The purpose of our study was to investigate KAI1 expression in the progression of human colorectal cancer. We first analyzed 20 colorectal cancer cell lines by immunoblot techniques. KAI1 was expressed heterogeneously, with the tumor cell lines having a more complex degree of glycosylation compared with that of the normal colonic tissue. KAI1 was highly expressed in the primary SW480 colon cancer cell line but was down-regulated 15-fold in the matched metastatic SW620 cell line. We also investigated KAI1 protein expression by immunohistochemistry in tissues from 84 patients with colorectal cancer. Each tissue section was assigned a KAI1 mean score (KMS) from 0 to 300 based on the product of the percentage of cells that stained for KAI1 and the intensity of the stain (1, 2, or 3). In 84 patients with colorectal cancer, KAI1 was expressed at high levels in normal colonic mucosa (KMS 226) but was expressed at lower levels in the primary tumors (KMS 65; P < 0.0001). In a subset of 12 patients with stage IV metastatic disease, we observed a progressive down-regulation of KAI1, from the normal adjacent colonic mucosa (KMS 193) to the primary tumor (KMS 72; P = 0.0001) to the liver metastasis (KMS 25; tumor compared with metastasis, P = 0.0135). We found no correlation between loss of KAI1 expression and stage of disease. In 10 patients, we also noted loss of KAI1 expression in the transition from normal colonic mucosa (KMS 237) to adenoma (KMS 174) to carcinoma (KMS 62; P < 0.0167 for all three comparisons). We conclude that the down-regulation of KAI1 occurs early in the progression of colorectal cancer.
Do What I Want, Not What I Did: Imitation of Skills by Planning Sequences of Actions (2016)

We propose a learning-from-demonstration approach for grounding actions from expert data and an algorithm for using these actions to perform a task in new environments. Our approach is based on an application of sampling-based motion planning to search through the tree of discrete, high-level actions constructed from a symbolic representation of a task. Recursive sampling-based planning is used to explore the space of possible continuous-space instantiations of these actions. We demonstrate the utility of our approach with a magnetic structure assembly task, showing that the robot can intelligently select a sequence of actions in different parts of the workspace and in the presence of obstacles. This approach can better adapt to new environments by selecting the correct high-level actions for the particular environment while taking human preferences into account.
821 A High Accuracy Analysis Method for Rotor Vibration Using Equivalent Reduced Model of Solid Model (2012)

The natural frequency calculated by a conventional beam theory technique of a stepped rotor whose diameter is not constant has a tendency to become high. For this subject, the shaft stiffness evaluation method which uses a stepped rotor shape was proposed. Concretely, after generating a solid model from the shape data of a stepped rotor, stiffness of the solid model is calculated, next, all degree of freedom of the solid model is reduced to the degree of freedom of the contact face, and high accuracy equivalent reduced model stiffness is introduced by the technique reducing the degree of freedom of the contact face to the degree of freedom of the beam model. After the verification result of a simple model by this method is described, the comparison of the numerical natural frequency and the measured result of a turbine rotor is reported.