gebhart/patrepeval huggingface dataset:
Optimizing Protein Coordination to Quantum Dots with Designer Peptidyl Linkers (2013)

Semiconductor quantum dots (QDs) demonstrate select optical properties that make them of particular use in biological imaging and biosensing. Controlled attachment of biomolecules such as proteins to the QD surface is thus critically necessary for development of these functional nanobiomaterials. QD surface coatings such as poly(ethylene glycol) impart colloidal stability to the QDs, making them usable in physiological environments, but can impede attachment of proteins due to steric interactions. While this problem is being partially addressed through the development of more compact QD ligands, here we present an alternative and complementary approach to this issue by engineering rigid peptidyl linkers that can be appended onto almost all expressed proteins. The linkers are specifically designed to extend a terminal polyhistidine sequence out from the globular protein structure and penetrate the QD ligand coating to enhance binding by metal-affinity driven coordination. α-Helical linkers of two lengths terminating in either a single or triple hexahistidine motif were fused onto a single-domain antibody; these were then self-assembled onto QDs to create a model immunosensor system targeted against the biothreat agent ricin. We utilized this system to systematically evaluate the peptidyl linker design in functional assays using QDs stabilized with four different types of coating ligands including poly(ethylene glycol). We show that increased linker length, but surprisingly not added histidines, can improve protein to QD attachment and sensor performance despite the surface ligand size with both custom and commercial QD preparations. Implications for these findings on the development of QD-based biosensors are discussed.
Hybrid rotary-translational vibration energy harvester using cycloidal motion as a mechanical amplifier (2014)

This paper reports on a hybrid rotary-translational vibration energy harvesting approach that exploits cycloidal motion to achieve a relatively high power density from an oscillatory kinetic energy harvester operating at frequencies below 10 Hz. The approach uses a rolling magnetic sphere. The rolling motion mechanically amplifies the velocity at which the magnetic pole of the sphere passes a nearby coil transducer, inducing a proportionally larger electro-motive force across the coil. A prototype cycloidal energy harvester is shown to produce a peak power of 201 mW from a host vibration of 500 mg rms at 5.4 Hz.
Doubly tuned local coils for MRI and MRS at 1.5 T (1988)

We describe a doubly tuned radiofrequency (RF) local coil probe designed specifically for performing in vivo image-localized spectroscopy. The probe was designed using principles developed in connection with the counter-rotating-current (CRC) and planar-pair loop gap resonators for magnetic resonance imaging (MRI). The probe design satisfies several criteria useful for in vivo 1H/31P experiments at 1.5 T. First, sensitivity on the low-frequency mode is preserved relative to a singly tuned coil. This result was confirmed by bench-test and in vitro MR experimental data. Second, through principles of intrinsic decoupling the probe is isolated from any externally applied uniform excitation field, which is desirable for in vivo 1H imaging and solvent suppression. Third, the regions of sensitivity of the high- and low-frequency modes of the coil are similar, and therefore spectroscopic volumes of interest identified on an image will reflect the same volumes as those selected during spectroscopy. Finally, interface to the MR system is such that the high- or low-frequency circuits may be selected entirely under software control, with no requirement for changing coils or cables or moving the subject.
ChemInform Abstract: 9‐Amino‐1,2,3,4‐tetrahydroacridin‐1‐ols: Synthesis and Evaluation as Potential Alzheimer′s Disease Therapeutics. (1990)

Abstract The anthranilic nitriles (I) are coupled with the diketone (II) to give the enamines (III) which are cyclized, forming the acridones (IV).
Theory of simultaneous control of orientation and translational motion of nanorods using positive dielectrophoretic forces (2005)

The manipulation of individual submicron-sized objects has been the focus of significant efforts over the last few years. A method to arbitrarily move and orient a set of rod-shaped conductive particles in a region defined by a set of electrodes using positive dielectrophoretic forces is presented. While the orientation of each particle is directly specified through the angle of the local electric field, its position is indirectly controlled through the applied force. Each electrode is approximated as an unknown point charge and an induced dipole. Since each induced dipole results from the combination of all other sources, a set of linear constraints are derived to enforce the self-consistency of the system. Additionally, the force and orientation of each particle also form an additional set of linear constraints. This combined set of constraints is then solved numerically to yield the sources required to induce the desired orientation and motion of each particle. It is observed that the minimum number of electrodes that can be used to control a set of N particles is 4N+1. Numerical simulations demonstrate that the control of a single nanorod (diameter of 70nm; length of 1.4μm) in the midst of a realistic electrode array can be accomplished under practical conditions. In addition, such control of orientation and motion can be achieved over an ample region in the vicinity of each rod.
Characterization of N-Linked Glycosylation on Recombinant Glycoproteins Produced in Pichia pastoris Using ESI-MS and MALDI-TOF (2008)

The production of recombinant therapeutic glycoproteins is an active area of research and drug development. Typically, improvements in therapeutic glycoprotein efficacy have focused on engineering additional N-glycosylation sites into the primary amino acid sequence or attempting to control a particular glycoform profile on a protein through process improvements. Recently, a number of alternative expression systems have appeared that are challenging the dominance of mammalian cell culture. Our laboratory has focused on the re-engineering of the secretory pathway in the yeast Pichia pastoris to perform glycosylation reactions that mimic processing of N-glycans in humans. We have demonstrated that human antibodies with specific human N-glycan structures can be produced in glycoengineered lines of Pichia pastoris and that antibody-mediated effector functions can be optimized by generating specific glycoforms. In this chapter we provide detailed protocols for the analysis of glycosylation on intact glycoproteins by MALDI-TOF and site specific N-glycan occupancy on digested glycoprotein using ESI-MS.
Eyemotion: Classifying Facial Expressions in VR Using Eye-Tracking Cameras (2019)

One of the main challenges of social interaction in virtual reality settings is that head-mounted displays occlude a large portion of the face, blocking facial expressions and thereby restricting social engagement cues among users. We present an algorithm to automatically infer expressions by analyzing only a partially occluded face while the user is engaged in a virtual reality experience. Specifically, we show that images of the user's eyes captured from an IR gaze-tracking camera within a VR headset are sufficient to infer a subset of facial expressions without the use of any fixed external camera. Using these inferences, we can generate dynamic avatars in real-time which function as an expressive surrogate for the user. We propose a novel data collection pipeline as well as a novel approach for increasing CNN accuracy via personalization. Our results show a mean accuracy of 74% (F1 of 0.73) among 5 'emotive' expressions and a mean accuracy of 70% (F1 of 0.68) among 10 distinct facial action units, outperforming human raters.
Sparsity Enhanced Mismatch Model for Robust Intercell Interference Management in Heterogeneous Networks With Doubly-Selective Fading Channels (2015)

Transmission over doubly-selective fading (DSF) interference channel often relies on the use of robust precoder due to a lack of accurate channel state information, with performance often depending on the conservativeness of the mismatch model. Previously proposed mismatch models either have been deemed too conservative (deterministic models) or are prone to error due to inaccuracy in the probability density function (pdf) and corresponding parameters (stochastic models). A deterministic mismatch model called Sparsity Enhanced Mismatch Model - Reverse discrete prolate spheroidal sequence, or SEMMR, is proposed herein in an attempt to alleviate this problem. Different from all previously deterministic models, the proposed model exploits the inherent sparse characteristics of DSF interference channels which lead to a two-stage robust transceiver design that outperforms precoding only strategy incorporating conventional norm ball mismatch model (NBMM). The inherent sparsity in the channel is brought forth by modeling the channel using a basis expansion model (BEM) where discrete prolate spheroidal sequence (DPSS) is used as a basis. Analytical and simulation results are provided to validate the performance gains of the SEMMR transceiver over the NBMM precoder.
TAE226‐Induced apoptosis in breast cancer cells with overexpressed Src or EGFR (2007)

Focal adhesion kinase, FAK is a 125 kDa nonreceptor tyrosine kinase that localizes to focal adhesions. FAK is overexpressed in human tumors and regulates cellular adhesion and survival signaling. We have shown previously that the dominant-negative FAK, C-terminal FAK-CD, caused detachment and apoptosis in human breast cancer cells, and that overexpression of an activated form of Src tyrosine kinase or epidermal growth factor receptor, EGFR, suppressed FAK-CD induced apoptotic effects in breast cancer cells. In the present study, we studied the effect of a novel FAK inhibitor, TAE226 (Novartis, Inc.), on the breast cancer cell lines. We used stable breast cancer cell lines overexpressing Src (MCF-7-Src and BT474-Src) or overexpressing EGFR (BT474-EGFR), and control breast cancer cell lines for the treatment with different doses of TAE226 drug. The detachment and apoptosis caused by TAE226 was analyzed and compared with the effect of the dominant-negative adenoviral FAK-CD. The TAE226 drug caused a dose-dependent increase of detachment and apoptosis in both BT474 and MCF-7-Vector and Src cells and in BT474-EGFR and BT474-pcDNA3 cells. Additionally, TAE226 caused downregulation of Y397-FAK, FAK and activation of PARP or caspase-3 proteins. Both Src and EGFR-overexpressing cells were not resistant to the TAE226 treatment compared to FAK-CD treatment. In addition, normal breast MCF-10A cell line was resistant to both TAE226 drug and to the Ad-FAK-CD inhibitor. Thus, inhibition of autophosphorylation activity of FAK with the TAE226 inhibitor at 10-20 microM is effective in causing apoptosis in breast cancer cells, resistant to the Ad-FAK-CD inhibitor that can be used effectively in therapy.
Supplemental Dataset 2 from Detecting the Presence and Progression of Premalignant Lung Lesions via Airway Gene Expression (2023)

<p>Results of pathway enrichment using ROAST (FDR<0.05). The column "Direction" refers to pathway enrichment among genes up-regulated (Up) or down-regulated (Down) in the presence of PMLs.</p>
PROTECTANT FOR WOOD (1976)

According to the patent application, substances, particularly wood, which are normally subject to deterioration due to marine borers, are preserved by applying to the substance a dibutylbenzylphenol.
Fast kVp-switching dual energy CT for PET attenuation correction (2009)

X-ray CT images are used routinely for attenuation correction in PET/CT systems. However, conventional CT-based attenuation correction (CTAC) can be inaccurate in regions containing iodine contrast agent. Dual-energy (DE) CT has the potential to improve the accuracy of attenuation correction in PET, but conventional DECT can suffer from motion artifacts. Recent X-ray CT systems can collect DE sinograms by rapidly switching the X-ray tube voltage between two levels for alternate projection views, reducing motion artifacts. The goal of this work is to study statistical methods for image reconstruction from both fast kVp-switching DE scans and from conventional dual-rotate DE scans in the context of CTAC for PET.
Fluoroscopy-based laser projection system for surgical guidance and its calibration methods (2018)

We have developed a laser projection system, which can project laser on corresponding position to surgical planning drawn at a fluoroscopic image without an optical tracking system. In this paper, we introduce a spatial calibration method between a laser module and a fluoroscope for the laser projection and evaluate its accuracy with a mimic experimental system. The experimental system consists of a laser module, a distance measurement unit and a CCD camera. The laser modules can project arbitrary line on surface by reflecting a point source laser with two galvanometers. We designed a calibration phantom by combining a collimator for accurate laser pattern positioning and stainless steel ball arrays for calculation of an extrinsic parameter of a C-arm fluoroscopy. We set a projection plane having ruler in 400mm distance from the CCD camera, and set 54 points on the screen. The laser module projects points with respect to the set points, and a distance error between set points and projected points and angular error are calculated. The distance errors is 1.5±1.9 mm (average ± standard deviation). Maximum error was 7.5 mm. Angular error was smaller than 2 degrees. The laser projection system and its calibration method shows clinically acceptable accuracy and the clinical application is the next step.
Flow energy piezoelectric bimorph nozzle harvester (2014)

There is a need for a long-life power generation scheme that could be used downhole in an oil well to produce 1 Watt average power. There are a variety of existing or proposed energy harvesting schemes that could be used in this environment but each of these has its own limitations. The vibrating piezoelectric structure is in principle capable of operating for very long lifetimes (decades) thereby possibly overcoming a principle limitation of existing technology based on rotating turbo-machinery. In order to determine the feasibility of using piezoelectrics to produce suitable flow energy harvesting, we surveyed experimentally a variety of nozzle configurations that could be used to excite a vibrating piezoelectric structure in such a way as to enable conversion of flow energy into useful amounts of electrical power. These included reed structures, spring mass-structures, drag and lift bluff bodies and a variety of nozzles with varying flow profiles. Although not an exhaustive survey we identified a spline nozzle/piezoelectric bimorph system that experimentally produced up to 3.4 mW per bimorph. This paper will discuss these results and present our initial analyses of the device using dimensional analysis and constitutive electromechanical modeling. The analysis suggests that an order-of-magnitude improvement in power generation from the current design is possible.
Sodium tungstate decreases sucrase and Na<sup>+</sup>/<scp>d</scp>-glucose cotransporter in the jejunum of diabetic rats (2008)

Sodium tungstate reduces glycemia and reverts the diabetic phenotype in several induced and genetic animal models of diabetes. Oral administration of this compound has recently emerged as an effective treatment for diabetes. Here we examined the effects of 30 days of oral administration of tungstate on disaccharidase and Na+/D-glucose cotransporter (SGLT1) activity in the jejunum of control and streptozotocin-induced diabetic rats. Diabetes increased sucrase-specific activity in the jejunal mucosa but did not affect the activity of lactase, maltase, or trehalase. The abundance and the maximal rate of transport of SGLT1 in isolated brush-border membrane vesicles also increased. Tungstate decreased sucrase activity and normalized SGLT1 expression and activity in the jejunum of diabetic rats. Furthermore, tungstate did not change the affinity of SGLT1 for d-glucose and had no effect on the diffusional component. In control animals, tungstate had no effect on disaccharidases or SGLT1 expression. Northern blot analysis showed that the amount of specific SGLT1 mRNA was the same in the jejunum from all experimental groups, thereby indicating that changes in SGLT1 abundance are due to posttranscriptional mechanisms. We conclude that the antidiabetic effect of tungstate is partly due to normalization of the activity of sucrase and SGLT1 in the brush-border membrane of enterocytes.
The weakest failure detector for solving consensus (1996)

We determine what information about failures is necessary and sufficient to solve Consensus in asynchronous distributed systems subject to crash failures. In Chandra and Toueg [1996], it is shown that W , a failure detector that provides surprisingly little information about which processes have crashed, is sufficient to solve Consensus in asynchronous systems with a majority of correct processes. In this paper, we prove that to solve Consensus, any failure detector has to provide at least as much information as W. Thus, W is indeed the weakest failure detector for solving Consensus in asynchronous systems with a majority of correct processes.
History Matching Reservoir Models Simulated from the Pluri-Gaussian Method (2005)

Abstract Gaussian-related random realizations are widely used in petroleum engineering to describe permeability or porosity distributions in underground reservoirs. Except by luck, flow simulations run for these realizations do not yield numerical answers reproducing the measured dynamic data such as well pressures, flow rates, water cuts… Realizations must be modified to become consistent with the field data, which is done through an optimization process. The gradual deformation method (GDM) is a geostatistical parameterization technique introduced to change continuously Gaussian-related realizations from a few parameters while preserving the two-order statistics. In this paper, we focus on realizations simulated from the pluri-Gaussian method and we show how to apply the GDM to modify such realizations. The pluri-Gaussian method, which is an extension of the truncated Gaussian method, is used for generating facies realizations. It shows the same general features as the truncated Gaussian method, but with a wider range of possibilities especially in terms of complexity for the generated realizations, making it possible to better represent reservoir heterogeneity. The simplest scheme followed by the pluri-Gaussian method, which is presented here, involves the transformation of two starting Gaussian realizations. The GDM can be exploited to modify both realizations independently or simultaneously. Additionally, this modification may be global or local. In other words, the GDM can be used to change the whole pluri-Gaussian realization by globally changing either one or both of the starting Gaussian realizations. It can be used also to change given subdomains of the pluri-Gaussian realization by locally changing either one or both of the starting Gaussian realizations. This capability provides a substantial flexibility to the matching process. The suggested methodology is validated on synthetic test cases, which stress the efficiency of the suggested methodology in terms of model simulation and history matching.
W-N type gear tooth profile in view of the radius curvature. (1989)

The feature of W-N (Wildhaber-Novikov) gear is that the engagement of tooth surfaces becomes a contact between concave and convex surfaces, resulting in small relative curvature and high surface durability. However, this gear has a defect that it is very sensitive to the center distance error. So, we developed the tooth profile that causes it to become insensitive to the center distance error without injuring the advantages of the W-N gears. We clarified that the relationship between the change in the center distance and the operating pressure angle differs depending upon the rate of change of radius curvature of the tooth profile, and studied and indicated the tooth profile having what radius curvature is suitable for the W-N type gears.
A Framework for Autonomous Robot Deployment with Perfect Demand Satisfaction using Virtual Forces (2019)

In many applications, robots autonomous deployment is preferable and sometimes it is the only affordable solution. To address this issue, virtual force (VF) is one of the prominent approaches to performing multirobot deployment autonomously. However, most of the existing VF-based approaches consider only a uniform deployment to maximize the covered area while ignoring the criticality of specific locations during the deployment process. To overcome these limitations, we present a framework for autonomously deploy robots or vehicles using virtual force. The framework is composed of two stages. In the first stage, a two-hop Cooperative Virtual Force based Robots Deployment (Two-hop COVER) is employed where a cooperative relation between robots and neighboring landmarks is established to satisfy mission requirements. The second stage complements the first stage and ensures perfect demand satisfaction by utilizing the Trace Fingerprint technique which collected traces while each robot traversing the deployment area. Finally, a fairness-aware version of Two-hop COVER is presented to consider scenarios where the mission requirements are greater than the available resources (i.e. robots). We evaluate our framework via extensive simulations. The results demonstrate outstanding performance compared to contemporary approaches in terms of total travelled distance, total exchanged messages, total deployment time, and Jain fairness index.
Efficient hardware implementation of an image compressor for wireless capsule endoscopy applications (2008)

The paper presents an area- and power-efficient implementation of an image compressor for wireless capsule endoscopy application. The architecture uses a direct mapping to compute the two-dimensional Discrete Cosine Transform which eliminates the need of transpose operation and results in reduced area and low processing time. The algorithm has been modified to comply with the JPEG standard and the corresponding quantization tables have been developed and the architecture is implemented using the CMOS 0.18um technology. The processor costs less than 3.5k cells, runs at a maximum frequency of 150 MHz, and consumes 10 mW of power. The test results of several endoscopic colour images show that higher compression ratio (over 85%) can be achieved with high quality image reconstruction (over 30 dB).
Development of magnetic levitated stage for wide area movements (2007)

This paper proposes a magnetic levitation system without other assistant devices that can move in wide area (< 300times300 mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> ) as well as in high precision (< plusmn100 nm).