gebhart/patrepeval huggingface dataset:
LipidHunter Identifies Phospholipids by High-Throughput Processing of LC-MS and Shotgun Lipidomics Datasets (2017)

Lipids are dynamic constituents of biological systems, rapidly responding to any changes in physiological conditions. Thus, there is a large interest in lipid-derived markers for diagnostic and prognostic applications, especially in translational and systems medicine research. As lipid identification remains a bottleneck of modern untargeted lipidomics, we developed LipidHunter, a new open source software for the high-throughput identification of phospholipids in data acquired by LC-MS and shotgun experiments. LipidHunter resembles a workflow of manual spectra annotation. Lipid identification is based on MS/MS data analysis in accordance with defined fragmentation rules for each phospholipid (PL) class. The software tool matches product and neutral loss signals obtained by collision-induced dissociation to a user-defined white list of fatty acid residues and PL class-specific fragments. The identified signals are tested against elemental composition and bulk identification provided via LIPID MAPS search. Furthermore, LipidHunter provides information-rich tabular and graphical reports allowing to trace back key identification steps and perform data quality control. Thereby, 202 discrete lipid species were identified in lipid extracts from rat primary cardiomyocytes treated with a peroxynitrite donor. Their relative quantification allowed the monitoring of dynamic reconfiguration of the cellular lipidome in response to mild nitroxidative stress. LipidHunter is available free for download at https://bitbucket.org/SysMedOs/lipidhunter .
The ADAM design planning engine (1991)

A novel paradigm for managing the digital process is presented. Under this paradigm, design is seen as a process in which abstract models of design tools are applied to abstract models of design states in a simulated or planning space, until a sequence of design tasks has been constructed to completion. Important parameters of the hypothetical design represented by the terminal states are then estimated. Either the planning is then repeated, or the sequence, or plan, is then executed, or carried out, in an execution space. This execution is monitored for violation of expectations; if violations occur, control is returned to the planner. The knowledge base of the planner is populated with register-transfer level (RTL) concepts for digital system design; it can also be populated with other knowledge sets. The planner forms part of the USC advanced design automation (ADAM) system.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">></ETX>
The Illustrated encyclopedia of beekeeping (1985)

The illustrated encyclopedia of beekeeping , The illustrated encyclopedia of beekeeping , مرکز فناوری اطلاعات و اطلاع رسانی کشاورزی
Neuroprotectin D1-mediated anti-inflammatory and survival signaling in stroke, retinal degenerations, and Alzheimer's disease (2008)

Docosahexaenoic acid (DHA), the main omega-3 fatty acid, is concentrated and avidly retained in membrane phospholipids of the nervous system. DHA is involved in brain and retina function, aging, and neurological and psychiatric/behavioral illnesses. Neuroprotectin D1 (NPD1), the first-identified stereoselective bioactive product of DHA, exerts neuroprotection in models of experimental stroke by down-regulating brain ischemia reperfusion (BIR)-induced leukocyte infiltration, proinflammatory signaling, and infarct size. Moreover, NPD1 inhibits cytokine-mediated cyclooxygenase-2 (COX-2) expression. Photoreceptor membranes display the highest content of DHA of any cell. Retinal pigment epithelial cells participate in the phagocytosis of the tips of photoreceptor cells (photoreceptor outer segment renewal). There is a DHA retrieval-intercellular mechanism between both types of cells that conserves this fatty acid during this process. NPD1 promotes homeostatic regulation of the integrity of these two cells, particularly during oxidative stress, and this protective signaling may be relevant in retinal degenerative diseases. Moreover, neurotrophins are NPD1-synthesis agonists, and NPD1 content is decreased in the CA1 region of the hippocampus of Alzheimer's patients. Overall, NPD1 promotes brain cell survival via the induction of antiapoptotic and neuroprotective gene-expression programs that suppress Abeta42 production and its neurotoxicity. Thus, NPD1 elicits potent cell-protective, anti-inflammatory, prosurvival repair signaling.
Creation and discovery of ligand–receptor pairs for transcriptional control with small molecules (2004)

The nuclear receptor retinoid X receptor (RXR) is a ligand-activated transcription factor. To create receptors for a new ligand, a structure-based approach was used to generate a library of approximately 380,000 mutant RXR genes. To discover functional variants within the library, we used chemical complementation, a method of protein engineering that uses the power of genetic selection. Wild-type RXR has an EC50 of 500 nM for 9-cis retinoic acid (9cRA) and an EC50 of >10 microM for the synthetic retinoid-like compound LG335 in yeast. The library produced ligand-receptor pairs with LG335 that have a variety of EC50 values (40 nM to >2 microM) and activation levels (10-80% of wild-type RXR with 9cRA) in yeast. The variant I268V;A272V;I310L;F313M has an EC50 for LG335 of 40 nM and an EC50 for 9cRA of >10 microM in yeast. This variant has essentially the reverse ligand specificity of wild-type RXR and is transcriptionally active at a 10-fold-lower ligand concentration in yeast. This EC50 is 25-fold lower than the best receptor we have engineered through site-directed mutagenesis, Q275C;I310M;F313I. Furthermore, the variants' EC50 values and activation levels in yeast and mammalian cells correlate. This protein engineering method should be extendable to produce other functional ligand-receptor pairs, which can be selected and characterized from libraries within weeks. Coupling large library construction with chemical complementation could be used to engineer proteins that bind virtually any small molecule for conditional gene expression, applications in metabolic engineering, and biosensors and to engineer enzymes through genetic selection.
Microfluidics, Lung Surfactant, and Respiratory Disorders (2009)

The lungs are the major organs of the respiratory system and contain a branching network of airway tubes that become shorter, narrower, and more numerous as they penetrate deeper into the lung. The tracheobronchial tree comprises 3 major types of airways: cartilaginous bronchi, membranous bronchioles, and gas exchange alveolar ducts. Upper airways and terminal bronchioles act merely as conduits for the passage of gas, whereas respiratory bronchioles and alveolar ducts carry out both conducting and gas exchange functions. Airways less than 1 to 2 mm in diameter that include membranous, terminal, and respiratory bronchioles as well as alveolar ducts are known as distal airways.1 These airways have a very large total cross-sectional area and relatively low resistance to the flow of gas (~10% to 20% of the total lung resistance).2 Due to their small size and high compliance, distal airways are prone to instabilities and closure at low lung volumes (eg, at the end of expiration). To prevent these fine structures from collapse (atelectasis), secretory cells of alveolar and neighboring airway epithelium produce pulmonary surfactant that distributes at the surface of the liquid lining layer of distal lung epithelium.3,4 Functional surfactant reduces surface tension at the luminal air-liquid interface and, thus, maintains the patency of airways and alveoli at low lung volumes. The presence of hysteresis in the pressure-volume curve of the lung indeed reflects this point ( Figure 1 ): the pressure required to support a certain volume (V) of the lung units during deflation (P2) is smaller than that when lungs are inflated (P1)5. During deflation, the surfactant film is compressed and presumably a more compact layer of surfactant lipid molecules is present at the air-liquid interface, which results in a lower surface tension. Active surfactant at the luminal air-liquid …
Participation of the Human Sperm Proteasome in the Capacitation Process and Its Regulation by Protein Kinase A and Tyrosine Kinase1 (2009)

The proteasome is a multicatalytic cellular complex present in human sperm that plays a significant role during several steps of mammalian fertilization. Here, we present evidence that the proteasome is involved in human sperm capacitation. Aliquots of highly motile sperm were incubated with proteasome inhibitors MG132 or epoxomicin. The percentage of capacitated sperm, the chymotrypsin-like activity of the proteasome, cAMP content, and the pattern of protein phosphorylation were assayed by using the chlortetracycline hydrochloride assay, a fluorogenic substrate, the cAMP enzyme immunoassay kit, and Western blot analysis, respectively. Our results indicate that treatment of sperm with proteasome inhibitors blocks the capacitation process, does not alter cAMP concentration, and changes the pattern of protein phosphorylation. To elucidate how proteasome activity is regulated during capacitation, sperm were incubated with: 1) tyrosine kinase (TK) inhibitors (genistein or herbimycin A); 2) protein kinase (PK) A inhibitors or activators (H89 and Rp-cAMPS, and 8-Br-cAMP, respectively); or 3) PKC inhibitors (tamoxifen or staurosporin) at different capacitation times. The chymotrypsin-like activity and degree of phosphorylation of the proteasome were then assayed. The results indicate that sperm treatment with TK and PKA inhibitors significantly decreases the chymotrypsin-like activity of the proteasome during capacitation. Immunoprecipitation and Western blot results suggest that the proteasome is phosphorylated during capacitation in a TK- and PKA-dependent pathway. In conclusion, we suggest that the sperm proteasome participates in the capacitation process, and that its activity is modulated by PKs.
EasyRide: active transponders for a fare collection system (2001)

The EasyRide ticketing system relies on radio frequency identification cards or tags to monitor passenger access to public transportation. Cards equipped with a miniature radio communication module identify passengers and record the information necessary to collect fares. Passengers equipped with an electronic card can board vehicles without prior ticket purchase. Equipment installed on each vehicle automatically detects the card and registers the passenger's entry and exit locations. The collected data, which contains the card and vehicle identification, stop names, and time stamps, is then forwarded from the vehicle to a fare calculation and billing system. Passengers only need to carry the card in their pockets or luggage during the trip, and the whole access control process is executed unnoticeably.
<p>Living with Narcolepsy: Current Management Strategies, Future Prospects, and Overlooked Real-Life Concerns</p> (2020)

Narcolepsy is a neurological disorder of the sleep-wake cycle characterized by excessive daytime sleepiness (EDS), cataplexy, nighttime sleep disturbances, and REM-sleep-related phenomena (sleep paralysis, hallucinations) that intrude into wakefulness. Dysfunction of the hypocretin/orexin system has been implicated as the underlying cause of narcolepsy with cataplexy. In most people with narcolepsy, symptom onset occurs between the ages of 10 and 35 years, but because the disorder is underrecognized and testing is complex, delays in diagnosis and treatment are common. Narcolepsy is treated with a combination of lifestyle modifications and medications that promote wakefulness and suppress cataplexy. Treatments are often effective in improving daytime functioning for individuals with narcolepsy, but side effects and/or lack of efficacy can result in suboptimal management of symptoms and, in many cases, significant residual impairment. Additionally, the psychosocial ramifications of narcolepsy are often neglected. Recently two new pharmacologic treatment options, solriamfetol and pitolisant, have been approved for adults, and the indication for sodium oxybate in narcolepsy has been expanded to include children. In recent years, there has been an uptick in patient-centered research, and promising new diagnostic and therapeutic options are in development. This paper summarizes current and prospective pharmacological therapies for treating both EDS and cataplexy, discusses concerns specific to children and reproductive-age women with narcolepsy, and reviews the negative impact of health-related stigma and efforts to address narcolepsy stigma.
Design of traveling-wave field panel for pharmaceutical powders based on computer simulation of particle trajectories (1997)

A fundamental study of charged particle levitation and transport in a traveling-wave field was carried out with a view to design and manufacture a series of flatbed panels with embedded electrode arrangement. Fourier transformation technique has been used to provide boundary conditions for the numerical calculations of particle trajectories. From the analysis, a potential function can be extracted which gives a better approximation compared to the one given by Masuda's early work. The numerical method using finite element and finite difference technique to solve field and trajectories, respectively, has been employed with a well-designed user interface. The user interface for integrating both methods is of universal value on its own. Based on this study, a computer program is under development with three levels of accuracy. The first level with consideration of the first spatial harmonic is presented in this paper, which is sufficient for designing panel electrode arrangements for the confinement and transport of dry powders. For the advanced study of particle trajectories under higher harmonic vectors, levels 2 and 3 (currently under development) may be utilized to serve different user requirement of accuracy. A series of panel electrodes have been designed and manufactured based on the analyses presented in this paper. Using these panels, lactose powder samples were successfully levitated and transported in the desired direction. Experimental observation is in good agreement with the numerical results.
Influence of Linker Geometry on Uranyl Complexation by Rigidly Linked Bis(3-hydroxy-<i>N</i>-methyl-pyridin-2-one) (2010)

A series of bis(3-hydroxy-N-methyl-pyridin-2-one) ligands was synthesized, and their respective uranyl complexes were characterized by single crystal X-ray diffraction analyses. These structures were inspected for high-energy conformations and evaluated using a series of metrics to measure co-planarity of chelating moieties with each other and the uranyl coordination plane, as well as to measure coordinative crowding about the uranyl dication. Both very short (ethyl, 3,4-thiophene and o-phenylene) and very long (alpha,alpha'-m-xylene and 1,8-fluorene) linkers provide optimal ligand geometries about the uranyl cation, resulting in planar, unstrained molecular arrangements. The planarity of the rigid linkers also suggests there is a degree of pre-organization for a planar coordination mode that is ideal for uranyl-selective ligand design. Comparison of intramolecular N(amide)-O(phenolate) distances and (1)H NMR chemical shifts of amide protons supports earlier results that short linkers provide the optimal geometry for intramolecular hydrogen bonding.
Resolution of Syncope With Treatment of Sleep Apnea (2008)

Sleep apnea is a common disorder associated with obesity and related health problems. Although treatment of sleep apnea may relieve some autonomic symptoms, it is currently unknown whether treatment of sleep apnea is specifically associated with the resolution of orthostatism and syncope. Herein we describe a 73-year-old man who had recurrent episodes of syncope. An extensive work-up, including cardiac and neurologic consultations, failed to identify the cause. An objective sleep evaluation led to the diagnosis of sleep apnea. Accordingly, the patient was treated with continuous positive airway pressure, which resolved the syncopal episodes. This case report generates a potentially important hypothesis that recurrent syncope may be effectively treated, in part, by correcting apnea. In patients with recurrent syncope of unknown etiology, a diagnosis of sleep apnea should be considered.
Carrier confinement effect-driven channel design and achievement of robust electrical/photostability and high mobility in oxide thin-film transistors (2015)

Carrier confinement effect-driven channel structures promoted stability under photo-bias stress condition, which was attributed increased recombinations events between photo-ionized oxygen vacancies and charged electrons due to the effective carrier confinement.
Textiles (2012)

This chapter contains sections titled: Introduction The Beginnings: Reed Mats, Basketry, and Twined Cloth Textile Production and the Economic Fabric of a Nascent State Variations on a Theme: Kaunakes, Carpet, Tapestry, and Felt A Coat of Many Colors: Pigments and Dyeing Garments, Gifts, and the Social Life of Cloth Guide to Further Reading
An L-Sleeve L-Monopole Antenna Fitting a Shark-Fin Module for Vehicular LTE, WLAN, and Car-to-Car Communications (2018)

An L-sleeve L-monopole (LSLM) antenna fitting a shark-fin module is proposed for vehicular long-term evolution (LTE) communication. Starting with classical sleeve monopole antennas, a low-profile evolution is introduced to explain the working principle of the LSLM. The influence of the ground plane, placement position, and bent of the LSLM is analyzed to fit different shark-fin modules. Designed prototypes (the LSLM and bended LSLM) cover the frequency range of 698-2700 MHz (VSWR <; 3), which would serve major LTE standards. One tab monopole antenna covering the frequency range of 5-6 GHz can be integrated into the shark-fin module and provide services for wireless local area network and car-to-car communications. Low mutual coupling (lower than -23 dB) between the two antennas is achieved in the frequency range of 698-6000 MHz without any additional filters, and the design method is presented for better understanding the underlying physics. The proposed antenna is fabricated on an affordable printed circuit board, which is useful for vehicular applications.
Adaptive Multiplane Image Generation from a Single Internet Picture (2021)

In the last few years, several works have tackled the problem of novel view synthesis from stereo images or even from a single picture. However, previous methods are computationally expensive, specially for high-resolution images. In this paper, we address the problem of generating a multiplane image (MPI) from a single high-resolution picture. We present the adaptive-MPI representation, which allows rendering novel views with low computational requirements. To this end, we propose an adaptive slicing algorithm that produces an MPI with a variable number of image planes. We present a new lightweight CNN for depth estimation, which is learned by knowledge distillation from a larger network. Occluded regions in the adaptive-MPI are inpainted also by a lightweight CNN. We show that our method is capable of producing high-quality predictions with one order of magnitude less parameters compared to previous approaches. The robustness of our method is evidenced on challenging pictures from the Internet.
The poly-single crystalline silicon interface (1984)

Cross sectional transmission electron microscopy (TEM) reveals an amorphous interfacial region of the order of 2 nm thick between chemical vapor deposition-(CVD) deposited polycrystalline silicon films and the single-crystal silicon substrate. The continuity of this region varies from sample to sample and plays an important role in the effects produced by subsequent heat treatment. In cases where this interfacial layer is continuous, the deposited layer remains polycrystalline. When the region is discontinuous, complete epitaxial realignment of the poly is possible. The speed of realignment depends on the implanted arsenic dose and is much greater than reported for undoped films. Various impurities are also observed at the interface and correlate with the character of the interface.
A short‐step synthesis of naphtho[2,3‐<i>b</i>]furan‐4,9‐dione (1994)

Abstract Phthalic anhydride in THF was added to 3‐lithiofuran 2 in THF to give 3,3‐di‐(3‐furyl)‐1,3‐dihy‐droisobenzofuran‐1‐one 4 . On the other hand, 2 in THF was added to phthalic anhydride in THF to give 2‐(3‐furanoyl)benzoic acid 3 by the inverse addition method. Further, the parent naphtho[2,3‐ b ]furan‐4,9‐dione 1 was obtained from the reaction of 3 with two equimolar amounts of LDA.
4D Reconstruction of the Beating Embryonic Heart From Two Orthogonal Sets of Parallel Optical Coherence Tomography Slice-Sequences (2012)

Current methods to build dynamic optical coherence tomography (OCT) volumes of the beating embryonic heart involve synchronization of 2D+time slice-sequences acquired over separate heartbeats. Temporal registration of these sequences is performed either through gating or postprocessing. While synchronization algorithms that exclusively rely on image- intrinsic signals allow forgoing external gating hardware, they are prone to error accumulation, require operator-supervised correction, or lead to nonisotropic resolution. Here, we propose an image-based, retrospective reconstruction technique that uses two sets of parallel 2D+T slice-sequences, acquired perpendicularly to each other, to yield accurate and automatic reconstructions with isotropic resolution. The method utilizes the similarity of the data at the slice intersections to spatio-temporally register the two sets of slice sequences and fuse them into a high-resolution 4D volume. We characterize our method by using 1) simulated heart phantom datasets and 2) OCT datasets acquired from the beating heart of live cultured E9.5 mouse and E10.5 rat embryos. We demonstrate that while our method requires greater acquisition and reconstruction time compared to methods that use slices from a single direction, it produces more accurate and self-validating reconstructions since each set of reconstructed slices acts as a reference for the slices in the perpendicular set.
Twenty years of terahertz imaging [Invited] (2018)

The birth of terahertz imaging approximately coincides with the birth of the journal Optics Express. The 20<sup>th</sup> anniversary of the journal is therefore an opportune moment to consider the state of progress in the field of terahertz imaging. This article discusses some of the compelling reasons that one may wish to form images in the THz range, in order to provide a perspective of how far the field has come since the early demonstrations of the mid-1990's. It then focuses on a few of the more prominent frontiers of current research, highlighting their impacts on both fundamental science and applications.
Fingolimod promotes peripheral nerve regeneration via modulation of lysophospholipid signaling (2016)

Our findings provide in vivo evidence for direct effects of fingolimod on cells of the peripheral nervous system that may propagate nerve regeneration via a dual mode of action, differentially affecting axonal outgrowth and myelination by modulating relevant aspects of S1P and LPA signaling.