gebhart/patrepeval huggingface dataset:
Mass spectrometry and immobilized enzymes for the screening of inhibitor libraries (2000)

A technique has been developed to rapidly screen enzyme inhibitor candidates from complex mixtures, such as those created by combinatorial synthesis. Inhibitor libraries are screened by using immobilized enzyme technologies and electrospray ionization ion cyclotron resonance mass spectrometry. The library mixture is first sprayed into the mass spectrometer, and compounds are identified. The library is subsequently incubated with the immobilized enzyme of interest under the correct conditions (buffer, pH, temperature) by using an excess of enzyme to ensure a surplus of sites for ligand binding. The immobilized enzyme/inhibitor mixture is centrifuged, and an aliquot of supernatant is again analyzed by electrospray ionization mass spectrometry. Potential inhibitors are quickly identified by comparison of the spectra before and after incubation with the immobilized enzyme. Non-inhibitors show no change in ion intensity after incubation, whereas weak inhibitors exhibit a visible decrease in ion abundance. Once inhibitor candidates have been identified, the library is reinjected into the mass spectrometer, and tandem mass spectrometry is used to determine the structure of the inhibitor candidates as needed. This method has been successfully demonstrated by identifying inhibitors of the enzymes pepsin and glutathione S -transferase from a 19- and 17-component library, respectively. It is further shown that the immobilized enzyme can be recycled and reused for continuous screening of additional new libraries without adding additional enzyme.
A LIF-TOF STUDY OF IONIC CLUSTERS $C_{4}F_{6}^{+}-R_{n}$ (1989)

Author Institution: Laser Spectroscopy Facility, Department of Chemistry, The Ohio State University
Structure-Guided Improvement of a Dual HPIV3/RSV Fusion Inhibitor (2019)

Human parainfluenza virus 3 (HPIV3) and respiratory syncytial virus (RSV) are leading causes of lower respiratory tract infections. There are currently no vaccines or antiviral therapeutics to treat existing HPIV3 or RSV infections. We recently reported a peptide (VIQKI), derived from the C-terminal heptad repeat (HRC) domain of the HPIV3 fusion (F) glycoprotein that inhibits infection by both HPIV3 and RSV. The dual inhibitory activity of VIQKI is due to its unique ability to bind to the N-terminal heptad repeat (HRN) domains of both HPIV3 and RSV F, thereby preventing the native HRN-HRC interactions required for viral entry. Here we describe the structure-guided design of dual inhibitors of HPIV3 and RSV fusion with improved efficacy. We show that VIQKI derivatives possessing one (I456F) or two (I454F/I456F) phenylalanine substitutions near the N-terminus exhibit more stable assemblies with RSV HRN domain and enhanced antiviral efficacy against both HPIV3 and RSV infection. Co-crystal structures of the new Phe-substituted inhibitors co-assembled with HPIV3 or RSV HRN domains reveal that the I456F substitution makes intimate hydrophobic contact with the core trimers of both HPIV3 and RSV F.
The Design of a Cell-Phone Based Balance-Training Device (2009)

Postural imbalance can result from various vestibular (central and peripheral), neurological, orthopedic, and vascular disorders, as well as sensory conflicts, head injuries, infections, medications, and aging. Balance rehabilitation has been shown to improve the quality of life of individuals with balance disorders by facilitating the development of compensatory strategies which mitigate dizziness, improve balance, and increase the ability to perform activities of daily living. The goal of this work is to design a cell phone based balance training device that can be used in the home to assist a patient with therapist-assigned balance exercises or in an environment where access to balance therapy is limited (i.e., rural regions in the developing world). The prototype comprises an iPhone (iPhone SDK, Apple), an auxiliary pager motor (Samsung GH31-00154C), and an audio amplifier (Analog Devices SSM2301). Body motion is detected by on-board tri-axial accelerometers, and a tilt estimate is computed using a low-pass filter. The phone's native pager motor and an auxiliary pager motor are used to provide real-time vibrotactile cues of body tilt along a single axis. The phone is worn on the small of the back to provide anterior-posterior vibrotactile trunk tilt feedback during stance, and worn near the right hip to provide medial-lateral vibrotactile trunk tilt feedback during gait. Auditory files direct the user through a series of standard balance rehabilitation exercises. A summary of the user's performance is displayed on the phone's screen following completion of the exercise.
Nanoscopic dopamine transporter distribution and conformation are inversely regulated by excitatory drive and D2-autoreceptor activity (2021)

SUMMARY The nanoscopic organization and regulation of individual molecular components in presynaptic varicosities of neurons releasing modulatory volume neurotransmitters like dopamine (DA) remain largely elusive. Here we show by application of several super-resolution microscopy techniques to cultured neurons and mouse striatal slices, that the dopamine transporter (DAT), a key protein in varicosities of dopaminergic neurons, exists in the membrane in dynamic equilibrium between an inward-facing nanodomain-localized and outward-facing unclustered configuration. The balance between these configurations is inversely regulated by excitatory drive and by DA D2-autoreceptor activation in manner dependent on Ca 2+ -influx via N-type voltage-gated Ca 2+ -channels. The DAT nanodomains contain tens of transporters molecules and overlap with nanodomains of PIP2 (phosphatidylinositol-4,5-bisphosphate) but show little overlap with D2-autoreceptor, syntaxin-1 and clathrin nanodomains. Summarized, the data reveal a mechanism for rapid alterations in nanoscopic DAT distribution and show a striking link of this to the conformational state of the transporter.
Cloning and Identification of Arp1, an Actin‐Related Protein from Pneumocystis carinii (1995)

The complete Pneumocystis carinii Arp1 gene has been sequenced from two cDNA clones. The gene encodes a protein 385 bp in length with an estimated size of 45,000 kD. The A + T% for the Arp1 gene and a 900-bp sequence upstream of the gene were 63.7% and 70.3%, respectively. These values are consistent with A + T codon preference displayed by P. carinii and are similar to values reported for other P. carinii genes. The predicted amino acid sequence of the P. carinii Arp1 protein had a similarity of 87.6% with Neurospora crassa Arp1, 82.1% similarity with vertebrate centractin, and 71.2% similarity with the Saccharomyces cerevisiae Act5p. Expression of Arp1 mRNA in P. carinii was detectable via synthesis of cDNA and subsequent PCR amplification. Affinity purified antibodies against S. cerevisiae Act5p, and canine centractin recognized both the recombinantly expressed protein and a 45,000 kD protein in P. carinii nuclear extracts. The Arp1 gene is the second member of the actin multigene family that has been identified in P. carinii.
Human Transgene-Free Amniotic-Fluid-Derived Induced Pluripotent Stem Cells for Autologous Cell Therapy (2014)

The establishment of a reliable prenatal source of autologous, transgene-free progenitor cells has enormous potential in the development of regenerative-medicine-based therapies for infants born with devastating birth defects. Here, we show that a largely CD117-negative population of human amniotic fluid mesenchymal stromal cells (AF-MSCs) obtained from fetuses with or without prenatally diagnosed anomalies are readily abundant and have limited baseline differentiation potential when compared with bone-marrow-derived MSCs and other somatic cell types. Nonetheless, the AF-MSCs could be easily reprogrammed into induced pluripotent stem cells (iPSCs) using nonintegrating Sendai viral vectors encoding for OCT4, SOX2, KLF4, and cMYC. The iPSCs were virtually indistinguishable from human embryonic stem cells in multiple assays and could be used to generate a relatively homogeneous population of neural progenitors, expressing PAX6, SOX2, SOX3, Musashi-1, and PSA-NCAM, for potential use in neurologic diseases. Further, these neural progenitors showed engraftment potential in vivo and were capable of differentiating into mature neurons and astrocytes in vitro. This study demonstrates the usefulness of AF-MSCs as an excellent source for the generation of human transgene-free iPSCs ideally suited for autologous perinatal regenerative medicine applications.
A Study on the Consent of Descriptive, Commanded and Banned Injustice in the Xinaqin-LiangHan[先秦兩漢] (2023)

The purpose of this study is to examine the consiliency of ‘勿’, ‘毋’, ‘無’, ‘莫’ which combine descriptive negation, command and forbidden negation among the negative meanings of ancient Chinese. It is to provide the easyness of discrimination by providing the semantics of the word to the learners who complain of the discrimination of ‘勿’, ‘毋’, ‘無’, ‘莫’ having the meaning of the descriptive denial, command and forbidden denial. There are many previous studies on ‘勿’, ‘毋’, ‘無’, ‘莫’ and ‘勿’, ‘毋’, ‘無’, ‘莫’ still are being studied. As a diachronic consideration, there is a study on the prohibition markers of the period of Chinese in the period of Chinese in the modern times - focusing on ‘勿’, ‘毋’, ‘無’, ‘莫’. This study investigated the classification by the two-minute method of exemption and prohibition in the sense of the negative form of the 'lecture duty' aspect. The public consideration is “the” law.,This study analyzed the grammar function of negative adverbs '' specifically by using the literature statistical survey of ‘勿’, ‘毋’, ‘無’, ‘莫’. This study also analyzed the literary examples of the public disclosures and compared the discriminatory qualities of ‘勿’, ‘毋’, ‘無’, ‘莫’ and ‘勿’, ‘毋’, ‘無’, ‘莫’ based on the public disclosure.,Furthermore, the semantics of narrative denial, command or forbidden denial were analyzed and the differences in syntactic thoughts were analyzed.,This is to solve the discrimination difficulties of ancient Chinese learners and to analyze the grammar function of ‘勿’, ‘毋’, ‘無’, ‘莫’.
Using loss location and loss magnitude manipulation for slip gain tuning in field oriented induction machine controllers (2013)

This work investigates loss location and loss magnitude manipulation via slip gain tuning in indirect field oriented induction machine drives. By using finite element analysis (FEA), the spatial distribution of the losses and the extent to which the distribution is manipulated via control tuning of the slip gain is investigated. Practical slip gain tuning variations across the full operating range, such as low speed when convection-based heat transfer is less effective, as well as high speed, are investigated. In addition, the dynamic performance corresponding to loss location manipulation tuning is investigated and documented. In this work, it is seen that using inadequate slip gain for field orientation reduces the total rotor losses within the machine. There is an opportunity to balance the shift of rotor loss to stator loss with the marginal degradation in torque dynamic performance when the slip gain is reduced for loss location manipulation. This work leads to a systematic method for understanding how loss location and magnitude change as a function of indirect field oriented controller tuning, with a goal of expanding the controller tuning paradigm to add a loss location objective to the classical dynamic torque performance objective.
Multi-band carrier-less amplitude and phase modulation for highly bandlimited visible light communications &#x2014; Invited paper (2015)

In this paper we present new numerical results for the signal-to-noise ratio and bit error rate (BER) performances of multi-band carrier-less amplitude and phase (m-CAP) modulation in the context of a highly bandlimited visible light communications (VLC) link. Light-emitting diodes are used as the transmitter and are modelled in this work as an ideal first order analogue low-pass filter. The link bandwidth is given as unity, while the filter cut-off frequency is set to 0.1. The number of bands, or subcarriers, is selected as m = 1, 2, 5 and 10. Here, we show that under such a high bandwidth constraint, using m = 10 subcarriers can result in 40% and 17% improvement in bit rate compared to m = 1 and 2, and m = 5 subcarriers, respectively for the same BER target.
Example based English-Bengali machine translation using wordnet (2009)

In this paper we propose an architecture of EnglishBengali Example Based Machine Translation (EBMT) using WordNet. The proposed EBMT system has five steps: 1) Tagging 2) Parsing 3) Prepare the chunks of the sentence using sub-sentential EBMT 4) Using an efficient adapting scheme, match the sentence rule 5) Translate from Source Language (English) to Target Language (Bengali) in the chunk and generate with morphological analysis with the help of WordNet. Using the word senses given by the WordNet we can detect the ambiguity and improve the correctness of translation.
Streamlined Protocol for Deep Proteomic Profiling of FAC-sorted Cells and Its Application to Freshly Isolated Murine Immune Cells* (2019)

Proteomic profiling describes the molecular landscape of proteins in cells immediately available to sense, transduce, and enact the appropriate responses to extracellular queues. Transcriptional profiling has proven invaluable to our understanding of cellular responses; however, insights may be lost as mounting evidence suggests transcript levels only moderately correlate with protein levels in steady state cells. Mass spectrometry-based quantitative proteomics is a well-suited and widely used analytical tool for studying global protein abundances. Typical proteomic workflows are often limited by the amount of sample input that is required for deep and quantitative proteome profiling. This is especially true if the cells of interest need to be purified by fluorescence-activated cell sorting (FACS) and one wants to avoid <i>ex vivo</i> culturing. To address this need, we developed an easy to implement, streamlined workflow that enables quantitative proteome profiling from roughly 2 μg of protein input per experimental condition. Utilizing a combination of facile cell collection from cell sorting, solid-state isobaric labeling and multiplexing of peptides, and small-scale fractionation, we profiled the proteomes of 12 freshly isolated, primary murine immune cell types. Analyzing half of the 3e5 cells collected per cell type, we quantified over 7000 proteins across 12 key immune cell populations directly from their resident tissues. We show that low input proteomics is precise, and the data generated accurately reflects many aspects of known immunology, while expanding the list of cell-type specific proteins across the cell types profiled. The low input proteomics methods we developed are readily adaptable and broadly applicable to any cell or sample types and should enable proteome profiling in systems previously unattainable.
Integra as a Dermal Replacement in a Meshed Composite Skin Graft in a Rat Model: A One-Step Operative Procedure (2002)

Single-step application of meshed, thin, split thickness autograft over meshed Integra-derived dermal substitute allows more rapid wound closure with less contraction and more efficient use of graft donor skin than can be obtained with the commonly used two-step grafting procedure.
Controlled Release of Dexamethasone From an Intravitreal Delivery System Using Porous Silicon Dioxide (2016)

The porous silicon-based Dex delivery system (pSiO2-COO-Dex) can be administered safely into vitreous without toxicity. Dex release from the porous silicon particles was sustained for 2 months and was effective against VEGF-induced retinal vessel reaction.
Co-design of a MEMS-CMOS autonomous switched oscillator (2015)

This work presents the co-design and simulation of a self-excited MEMS-CMOS oscillator. The device consists of an electrostatic MEMS actuator, a DC source and a resistive circuit switched by the actuator's displacement. The MEMS device is modeled after an existing device. A CMOS circuit is proposed for the displacement detection and the switching mechanism. The oscillator is capable of sustaining oscillations autonomously and exhibiting periodic and aperiodic behavior. The proposed oscillator can process electronic as well as nonelectronic information. The oscillator behavior is highly sensitive to stimuli which makes it a good candidate to be used as an enhanced sensor or in systems of coupled oscillators.
Excess bone marrow mast cells constitutively express CD154 (CD40 ligand) in Waldenstrom's macroglobulinemia and may support tumor cell growth through CD154/CD40 pathway (2004)

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Evolution of Turbine Cooling (2017)

Turbine cooling is a battle between the desire for greater hot section component life and the techno-economic demands of the marketplace. Surprisingly little separates the haves from the have nots. The evolution of turbine cooling is loosely analogous to that of the Darwinian theory of evolution for animals, starting from highly simplistic forms and progressing to increasingly more complex designs having greater capabilities. Yet even with the several generations of design advances, limitations are becoming apparent as complexity sometimes leads to less robust outcomes in operation. Furthermore, the changing environment for operation and servicing of cooled components, both the natural and the imposed environments, are resulting in new failure modes, higher sensitivities, and more variability in life. The present paper treats the evolution of turbine cooling in three broad aspects including the background development, the current state-of-the-art, and the prospects for the future. Unlike the Darwinian theory of evolution however, it is not feasible to implement thousands of small incremental design changes, random or not, to determine the fittest for survival and advancement. Instead, innovation and experience are utilized to direct the evolution. Over the last approximately 50 years, advances have led to an overall increase in component cooling effectiveness from 0.1 to 0.7. Innovation and invention aside, the performance of the engine has always dictated which technologies advance and which do not. Cooling technologies have been aided by complimentary and substantial advancements in materials and manufacturing. The state-of-the-art now contains dozens of internal component cooling methods with their many variations, yet still relies mainly on only a handful of basic film cooling forms that have been known for 40 years. Even so, large decreases in coolant usage, up to 50%, have been realized over time in the face of increasing turbine firing temperatures. The primary areas of greatest impact for the future of turbine cooling are discussed, these being new engine operating environments, component and systems integration effects, revolutionary turbine cooling, revolutionary manufacturing, and the quantification of unknowns. One key will be the marriage of design and manufacturing to bring about the concurrent use of engineered micro cooling or transpiration, with the ability of additive manufacturing. If successful, this combination could see a further 50% reduction in coolant usage for turbines. The other key element concerns the quantification of unknowns, which directly impacts validation and verification of current state-of-the-art and future turbine cooling. Addressing the entire scope of the challenges will require future turbine cooling to be of robust simplicity and stability, with freeform design, much as observed in the “designs” of nature.
Investigation of magnetic coupling in sputtered epitaxial Fe/Cr and Co/Cu wedged structures (1996)

We explore the magnetic interlayer exchange coupling in single-crystalline Fe/Cr and Co/Cu wedged multilayers prepared by magnetron sputtering on two orientations of MgO—(100) and (110). Structural examination shows that high quality epitaxial films are obtained in both systems using seeded epitaxy growth techniques. Oscillatory interlayer coupling is observed in Cr-wedged samples grown on both MgO(100) and MgO(110) with similarly long oscillation periods of ∼18 Å. These results are comparable to earlier work for molecular beam epitaxy and sputter-deposited epitaxial Fe/Cr structures. Long-period oscillatory coupling is also observed in sputtered Co/Cu(110) for the Cu-wedged structures. Studies of the dependence of magnetic coupling on the thickness of the magnetic layers for fixed Cr layer thickness provides no evidence of any nonmonotonic dependence.
An LED Light Source and Novel Fluorophore Combinations Improve Fluorescence Laparoscopic Detection of Metastatic Pancreatic Cancer in Orthotopic Mouse Models (2012)

Using an LED light source with adjustments to the red, blue, and green wavelengths, it is possible to simultaneously identify tumor metastases expressing fluorescent proteins of different wavelengths, which greatly enhanced the signal without compromising background illumination. Development of this fluorescence laparoscopy technology for clinical use can improve staging and resection of pancreatic cancer.
A surrogate-based uncertainty quantification with quantifiable errors (2012)

Surrogate models are often employed to reduce the computational cost required to complete uncertainty quantification, where one is interested in propagating input parameters uncertainties throughout a complex engineering model to estimate responses uncertainties. An improved surrogate construction approach is introduced here which places a premium on reducing the associated computational cost. Unlike existing methods where the surrogate is constructed first, then employed to propagate uncertainties, the new approach combines both sensitivity and uncertainty information to render further reduction in the computational cost. Mathematically, the reduction is described by a range finding algorithm that identifies a subspace in the parameters space, whereby parameters uncertainties orthogonal to the subspace contribute negligible amount to the propagated uncertainties. Moreover, the error resulting from the reduction can be upper-bounded. The new approach is demonstrated using a realistic nuclear assembly model and compared to existing methods in terms of computational cost and accuracy of uncertainties. Although we believe the algorithm is general, it will be applied here for linear-based surrogates and Gaussian parameters uncertainties. The generalization to nonlinear models will be detailed in a separate article. (authors)
Photomask repeater strategy for high-quality and low-cost reticle fabrication (2003)

The severe mask specification makes mask cost increase drastically. Especially, the increase in the mask cost deals ASIC businesses a fatal blow due to its small chip volume per product. Pattern writing cost has always occupied the main part of the prime mask cost and the emphasis of this is still increasing. This paper reports on a <i>Photomask Repeater</i> strategy to be a solution for reducing mask cost in pattern writing, comparing with conventional EB system.