gebhart/patrepeval huggingface dataset:
Biosynthesis of phosphatidylinositol-glycan (PI-G)-anchored membrane proteins in cell-free systems: cleavage of the nascent protein and addition of the PI-G moiety depend on the size of the COOH-terminal signal peptide. (1992)

Nascent translation products of PI-G-anchored membrane proteins contain both NH2- and COOH-terminal signal sequences of approximately 15-30 residues that are removed during processing. Removal of the latter occurs concomitant with the addition of the PI-G moiety to the newly formed COOH terminus. In human placental alkaline phosphatase (PLAP) the COOH-terminal signal peptide contains 29 residues. An engineered form of PLAP, miniPLAP 208, containing the same NH2- and COOH-terminal signal peptides as PLAP, was used as a substrate for cell-free processing. A comparison was made with mutants (delta 202, delta 197, delta 184, and delta 179) truncated at the COOH terminus. Intact preprominiPLAP 208 and truncated delta 202 were processed to yield the same mature product which, by size and distribution between Triton X-114 and water before and after treatment with inositol-specific phospholipases, indicates that it contained the PI-G moiety. Mutants that were further truncated at the COOH terminus, miniPLAPs delta 197, delta 184, and delta 179, were processed only at their NH2 termini. Those portions of the COOH-terminal sequence in miniPLAPs delta 197 and delta 1984 that extended beyond residue 179 were not removed during processing.
Effects of Ho addition on the magnetic properties and temperature stability of sintered Nd-Fe-B magnets (2011)

(Pr-Nd)33.0-xHoxFebalCu0.20Al0.75B1.15(x=0,1,3,5) sintered magnets were prepared via conventional route.Effects of Ho addition on their magnetic properties and temperature stability were analyzed.The formation of α-Fe phase in Nd-Fe-B alloy ingots was effectively suppressed,the intrinsic coercivity was largely increased,the remanence was slightly reduced and the temperature stability was improved to a great extent by adding certain amounts of Ho.Sintered Nd-Fe-B magnets with 1~3% Ho addition possess small average grain size and relatively homogeneous grain size distribution,and exhibit satisfactory comprehensive properties.
Supplementary Figure from Therapy-Related Transcriptional Subtypes in Matched Primary and Recurrent Head and Neck Cancer (2023)

Supplementary Figure from Therapy-Related Transcriptional Subtypes in Matched Primary and Recurrent Head and Neck Cancer
Zero-crossing method for hard iron interference and zero drift compensation applied to magnetometers (2016)

This paper presents a zero-crossing method for two-axis magnetometers that compensates the measurement offsets when sensor outputs are distorted due to the time-varying hard-iron interference and zero drift effects. The compensation method is derived based on a Kalman filter which can be used for real-time estimation. The performance of proposed method is evaluated using HMR2300r magnetometer with a ferromagnetic turntable. The angle estimation error after compensation was on the order of 1 to 2 degrees.
An efficient algorithm for mapping imaging data to 3D unstructured grids in computational biomechanics (2012)

Geometries for organ scale and multiscale simulations of organ function are now routinely derived from imaging data. However, medical images may also contain spatially heterogeneous information other than geometry that are relevant to such simulations either as initial conditions or in the form of model parameters. In this manuscript, we present an algorithm for the efficient and robust mapping of such data to imaging-based unstructured polyhedral grids in parallel. We then illustrate the application of our mapping algorithm to three different mapping problems: (i) the mapping of MRI diffusion tensor data to an unstructured ventricular grid; (ii) the mapping of serial cyrosection histology data to an unstructured mouse brain grid; and (iii) the mapping of computed tomography-derived volumetric strain data to an unstructured multiscale lung grid. Execution times and parallel performance are reported for each case.
Thimerosal potentiates Ca2+ release mediated by both the inositol 1,4,5-trisphosphate and the ryanodine receptors in sea urchin eggs. Implications for mechanistic studies on Ca2+ signaling (1994)

Two intracellular Ca2+ release pathways are modulated by Ca2+ itself, namely Ca(2+)-induced Ca2+ release (classical CICR), and Ca(2+)-sensitized inositol 1,4,5-trisphosphate (InsP3)-induced Ca2+ release (CSIICR). Both of these pathways are thought to be important in generating cytosolic Ca2+ oscillations. Caffeine and the sulfhydryl reagent thimerosal (TMS) are frequently used as selective modulators of CICR and CSIICR, respectively. We have studied the modes of action of caffeine and TMS in sea urchin egg homogenates using the Ca2+ indicator fluo-3. Cyclic ADP-ribose (cADPR), the only known endogenous compound to cause Ca2+ release via the ryanodine receptor, was used as an agonist for the classical CICR pathway. cADPR and InsP3 each alone caused release of sequestered Ca2+. Coaddition of caffeine dose-dependently and dramatically enhanced Ca2+ release induced by cADPR. InsP3-induced Ca2+ release was not affected by caffeine, but it was amplified by TMS, indicating the existence of the CSIICR pathway in this preparation. Surprisingly, cADPR-induced Ca2+ release was also markedly potentiated by TMS. TMS alone caused a slow increase in Ca2+ release which was not inhibited by heparin and/or procaine, indicating that TMS-induced Ca2+ release was not due to the actions of endogenous agonists (InsP3 or cADPR) on their receptors. All observed actions of TMS were abolished by dithiothreitol. We conclude: 1) both the InsP3- and cADPR-controlled Ca2+ release pathways are potentiated by TMS, while caffeine is specific for the cADPR pathway, indicating that TMS cannot be used as a selective reagent for probing the CSIICR mechanism; and 2) the action of TMS on intracellular Ca2+ release is independent of endogenous Ca2+ channel agonists, suggesting a novel action of TMS possibly on intravesicular Ca2+ handling.
Perspectives in paramagnetic NMR of metalloproteins (2008)

NMR experiments and tools for the characterization of the structure and dynamics of paramagnetic proteins are presented here. The focus is on the importance of (13)C direct-detection NMR for the assignment of paramagnetic systems in solution, on the information contained in paramagnetic effects observed both in solution and in the solid state, and on novel paramagnetism-based tools for the investigation of conformational heterogeneity in protein-protein complexes or in multi-domain proteins.
Impact of Time-of-Flight PET on Whole-Body Oncologic Studies: A Human Observer Lesion Detection and Localization Study (2011)

A combination of longer scan time (3 min in this study) and TOF imaging provides the best performance for imaging large patients or a low-uptake lesion in small or large patients. This imaging protocol also provides similar performance for all patient sizes for lesions in the same organ type with similar relative uptake, indicating an ability to provide a uniform clinical diagnosis in most oncologic lesion detection tasks.
Process control structures for multiprocessors (2002)

Describes a new approach to implementing and using a 'process' abstraction in multiprocessors. A new paradigm is described for virtual machines which are built out of finer granularity units called Resource Control Blocks (RCB). A collection of RCBs define a virtual machine. Each RCB is independently sharable. A user has the freedom to define a set of virtual machines each spanning a different collection of resources. Although the new paradigm offers additional flexibility, it carries no additional overhead when compared to previous implementations. Backwards compatible processes are scheduled and created with the same efficiency. New processes that carry less weight are created much more efficiently. A production system has been implemented and measured on Multimax, a shared-memory multiprocessor.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Adaptive prefetching for shared cache based chip multiprocessors (2009)

Chip multiprocessors (CMPs) present a unique scenario for software data prefetching with subtle tradeoffs between memory bandwidth and performance. In a shared L2 based CMP, multiple cores compete for the shared on-chip cache space and limited off-chip pin bandwidth. Purely software based prefetching techniques tend to increase this contention, leading to degradation in performance. In some cases, prefetches can become harmful by kicking out useful data from the shared cache whose next usage is earlier than the prefetched data, and the fraction of such harmful prefetches usually increases when we increase the number of cores used for executing a multi-threaded application code. In this paper, we propose two complementary techniques to address the problem of harmful prefetches in the context of shared L2 based CMPs. These techniques, namely, suppressing select data prefetches (if they are found to be harmful) and pinning select data in the L2 cache (if they are found to be frequent victim of harmful prefetches), are evaluated in this paper using two embedded application codes. Our experiments demonstrate that these two techniques are very effective in mitigating the impact of harmful prefetches, and as a result, we extract significant benefits from software prefetching even with large core counts.
A messy genetic algorithm for the vehicle routing problem with time window constraints (2002)

In vehicle routing problems with time window constraints (VRPTW), a set of vehicles with limited capacity, are to be routed from a central depot to a set of geographically dispersed customers with known demands and predefined time windows. To solve the problem, the optimized assignment of vehicles to each customer is needed as to achieve the minimal total cost without violating the capacity and time window constraints. Combinatorial optimization problems of this kind are NP-hard and are best solved to the near optimum by heuristics. The authors describe their research on a rare class of genetic algorithms, known as the messy genetic algorithms (mGA) in solving the VRPTW problem. The mGA has the merit of directly realizing the relational search needed in VRPTW representation, which cannot be easily realized using simple heuristic methods. The mGA was applied to solve the benchmark Solomon's 56 VRPTW 100-customer instances, and yielded 23 solutions better than or equivalent to the best solutions ever published in literature.
Calibrating for Ionospheric Phase Delays (1985)

Technique determines ionospheric phase delay on real-time universally applicable basis in terms of electrons per meter squared by coherently modulating two L-band carrier frequencies received from two Global Positioning System satelites. Two pseudorandom number sequences cross-correlated to derive delay time.
High-frequency, at-speed scan testing (2003)

The authors describe new strategies where at-speed scan tests can be applied with internal PLL. They present techniques for optimizing ATPG across multiple clock domains and methodologies to combine both stuck-at-fault and delay-test vectors into an effective test suite.
Multi- and single-target agents for major psychiatric diseases: therapeutic opportunities and challenges. (2008)

There is growing pressure to find more effective therapies for major psychiatric disorders, such as schizophrenia and depressive disorder. The repeated disappointments that have been experienced with highly selective, single-target agents have prompted questions about their relative merits. In contrast, a multi-target agent (MTA) approach, discovered either by serendipity or by judicious design, might offer a more rational way to address the complex clinical demands of patients and their co-morbidities. Rather than being mutually exclusive, a balanced portfolio of the two approaches may offer a beneficial and synergistic outcome toward identification of novel antipsychotic and antidepressant therapies. With improvements in biomarker technology, translational biology and a growing understanding of psychopathology, there is optimism that the new generation of MTAs will finally shed the stigma of 'dirty drugs' and progress to the concept of intentionally designed and tailored psychopharmacological agents.
The Immune Microenvironment in Mesothelioma: Mechanisms of Resistance to Immunotherapy (2019)

Although mesothelioma is the consequence of a protracted immune response to asbestos fibers and characterized by a clear immune infiltrate, novel immunotherapy approaches show less convincing results as compared to those seen in melanoma and non-small cell lung cancer. The immune suppressive microenvironment in mesothelioma is likely contributing to this therapy resistance. Therefore, it is important to explore the characteristics of the tumor microenvironment for explanations for this recalcitrant behavior. This review describes the stromal, cytokine, metabolic, and cellular milieu of mesothelioma, and attempts to make connection with the outcome of immunotherapy trials.
Sonochemical Deposition of Air-Stable Iron Nanoparticles on Monodispersed Carbon Spherules (2003)

A novel route was used to prepare “perfect spherical” monodispersed carbon with a smooth surface, which has a surface area of 8 m2/g. Air-stable iron nanoparticles with an average size of ∼10 nm were deposited on the surface of preformed carbon spherules with the aid of power ultrasound. This coating was achieved by ultrasonic irradiation of a slurry of carbon spherules and Fe(CO)5 in diphenylmethane for 90 min under an argon atmosphere. The as-prepared amorphous material was annealed in argon at 700 °C, forming air-stable iron deposited on carbon spherules. The product was characterized by XRD, TEM, EDAX, BET surface area, HR-SEM, TGA, DSC, magnetic measurements, electron paramagnetic resonance, and Raman spectroscopy.
Using human induced pluripotent stem cells to treat retinal disease (2013)

The eye is an ideal target for exploiting the potential of human induced pluripotent stem cell (hiPSC) technology in order to understand disease pathways and explore novel therapeutic strategies for inherited retinal disease. The aim of this article is to map the pathway from state-of-the art laboratory-based discoveries to realising the translational potential of this emerging technique. We describe the relevance and routes to establishing hiPSCs in selected models of human retinal disease. Additionally, we define pathways for applying hiPSC technology in treating currently incurable, progressive and blinding retinal disease.
Probing Local Electromechanical Effects in Highly Conductive (2012)

The functionality of a variety of materials and devices is strongly coupled with electromechanical effects which canbeusedtocharacterizetheirfunctionality.Ofhighinterestisthe investigation of these electromechanical effects on the nanoscale whichcanbeachievedbyusingscanningprobemicroscopy.Here,an electrical bias is applied locally to the scanning probe tip, and the mechanical sample response is detected. In some applications with electromechanical phenomena, such as energy storage or for biological samples, a liquid environment is required to provide full functionality and sample stability. However, electromechanical sample characterization has mostly been applied in air or under vacuum due to the difficultiesofapplyinglocalelectric fieldsinaconductiveenvironment.Here,wepresentadetailedstudyofpiezoresponseforcemicroscopyofferroelectric samples in liquid environments as a model system for electromechanical effects in general. The ionic strength of the liquid is varied, and possibilities and limitations of the technique are explored. Numerical simulations are used to explain the observed phenomena and used to suggest strategies to work in liquid environments with high ionic strength.
Robust human detection, tracking, and recognition in crowded urban areas (2014)

In this paper, we present algorithms we recently developed to support an automated security surveillance system for very crowded urban areas. In our approach for human detection, the color features are obtained by taking the difference of R, G, B spectrum and converting R, G, B to HSV (Hue, Saturation, Value) space. Morphological patch filtering and regional minimum and maximum segmentation on the extracted features are applied for target detection. The human tracking process approach includes: 1) Color and intensity feature matching track candidate selection; 2) Separate three parallel trackers for color, bright (above mean intensity), and dim (below mean intensity) detections, respectively; 3) Adaptive track gate size selection for reducing false tracking probability; and 4) Forward position prediction based on previous moving speed and direction for continuing tracking even when detections are missed from frame to frame. The Human target recognition is improved with a Super-Resolution Image Enhancement (SRIE) process. This process can improve target resolution by 3-5 times and can simultaneously process many targets that are tracked. Our approach can project tracks from one camera to another camera with a different perspective viewing angle to obtain additional biometric features from different perspective angles, and to continue tracking the same person from the 2nd camera even though the person moved out of the Field of View (FOV) of the 1st camera with ‘Tracking Relay’. Finally, the multiple cameras at different view poses have been geo-rectified to nadir view plane and geo-registered with Google- Earth (or other GIS) to obtain accurate positions (latitude, longitude, and altitude) of the tracked human for pin-point targeting and for a large area total human motion activity top-view. Preliminary tests of our algorithms indicate than high probability of detection can be achieved for both moving and stationary humans. Our algorithms can simultaneously track more than 100 human targets with averaged tracking period (time length) longer than the performance of the current state-of-the-art.
Involvement of proteasome b1i subunit, LMP2, on uterine leiomyosarcma tumorigenesis (2011)

Abstract Although the majority of smooth muscle neoplasms found in the uterus are benign, uterine leiomyosarcoma (LMS) is extremely malignant, with high rates of recurrence and metastasis. The development of gynecologic tumors is often correlated with secretion of female hormone; however, the development of human uterine LMS is not substantially correlated with hormonal conditions, and the risk factors are unclearly understood. Importantly, a diagnostic-biomarker, which distinguishes malignant human uterine LMS from benign tumor leiomyoma (LMA) is yet to be established. Accordingly, it is necessary to analyze risk factors associated with human uterine LMS, in order to establish a clinical treatment method. Homozygous deficient mice for a proteasome subunit b1i/LMP2 spontaneously develop uterine LMS, with a disease prevalence of ~40% by 14 months of age. Defective LMP2 expression in human uterine LMS was demonstrated, but present in human LMA. Therefore, loss in LMP2 expression may be one of the risk factors for human uterine LMS. LMP2 may be a potential diagnostic-biomarker and targeted- molecule for a new therapeutic approach.
Performance evaluation of a traceability system. An application to the radio frequency identification technology (2003)

The desire for reduced operation costs, high quality products and services, a better monitoring of items for a targeted intervention in case of critical situations and the increasing demand for security and safety from final consumers sets high requirements for well structured traceability systems. Advances in information technology permit synchronization between physical and information flows and coordination of activities among supply chain partners. Bar code and radio frequency identification (RFID) systems are examples of such technologies that permit us to collect data about logistics transactions of items, store and organize them in order to use this information in enterprises' management control, decision analysis and strategic planning systems. Within a company, the use of a specific item identification technology or the decision of switching from a technology to another is an important decision since it could have expensive consequences. The purpose of the paper is to provide a framework for identifying principles and functionalities of a traceability system in the context of a global supply chain. Using assessment criteria obtained by this analysis, we evaluate the performance of bar code and RFID systems. Finally, we describe benefits (measured as reduction in costs, improvement in the customer service level, etc.) that RFID technology can provide to supply chain processes.
Design and synthesis of 3,3′-biscoumarin-based c-Met inhibitors (2014)

A library of biscoumarin-based c-Met inhibitors was synthesized, based on optimization of 3,3'-biscoumarin hit 3, which was identified as a non-ATP competitive inhibitor of c-Met from a diverse library of coumarin derivatives. Among these compounds, 38 and 40 not only showed potent enzyme activities with IC50 values of 107 nM and 30 nM, respectively, but also inhibited c-Met phosphorylation in BaF3/TPR-Met and EBC-1 cells.
Analysis and design for ill-conditioned plants (1989)

Abstract A study is made of a special case of the robust performance problem given by Freudenberg (1989). When the weightings used to describe the uncertainty and performance specifications vary only with frequency, then it is possible to strengthen the results in the above-mentioned work by deriving both upper and lower bounds upon the structured singular value. Both sets of bounds are stated in terms of the coupling coefficients introduced by Freudenberg (1989), and essentially yield necessary and sufficient conditions for the structured singular value to be small. This information is used to suggest a strategy for compensator design to achieve robust performance despite plant ill-conditioning. Applying this strategy to an example, it can be seen how the design trade-offs quantified by the Bode gain-phase relation manifest themselves in the robust performance problem. Finally, the design is compared with one obtained using the'µ-synthesis' approach.
Some Properties of Phytochrome Isolated From Dark-grown Oat Seedlings (Avena sativa L.) (1968)

Phytochrome was partially purified from etiolated seedlings of Avena sativa L. Several properties of the red-absorbing (P(R)) and far-red absorbing (P(FR)) forms of the pigment were compared. The 2 forms could not be shown to differ with respect to their sedimentation velocity in sucrose density gradients, elution volume from Sephadex G-200 columns, binding properties on calcium phosphate, or electrophoretic mobility. P(FR), however, was more labile than P(R) during precipitation with 50% ammonium sulfate. Sephadex G-200 elution diagrams obtained with fresh phytochrome preparations revealed 2 components of different molecular weights, 1 roughly 180,000, and 1 roughly 80,000. Native phytochrome had an absorption spectrum in vivo showing an absorption maximum for P(R) of 667 nm. Both the large and small forms of phytochrome mentioned above can be maintained with an absorption maximum for P(R) of 667 nm. However, allowing them to remain for several hours as P(FR), even at 4 degrees , shifted this peak to 660 nm. The protein conformational change during phytochrome transformation may be quite small, though the various comparative techniques used do not strictly rule out a fairly large one. The need for maintaining the pigment as P(R) during all steps of purification, but particularly during ammonium sulfate precipitation is underscored.