gebhart/patrepeval huggingface dataset:
Identification of Amino Acid Residues Critical for Biological Activity in Human Interleukin-18 (2002)

Interleukin-18 (IL-18) is a pro-inflammatory cytokine, and IL-18-binding protein (IL-18BP) is a naturally occurring protein that binds IL-18 and neutralizes its biological activities. Computer modeling of human IL-18 identified two charged residues, Glu-42 and Lys-89, which interact with oppositely charged amino acid residues buried in a large hydrophobic pocket of IL-18BP. The cell surface IL-18 receptor alpha chain competes with IL-18BP for IL-18 binding, although the IL-18 receptor alpha chain does not share significant homology to IL-18BP. In the present study, Glu-42 was mutated to Lys and Lys-89 to Glu; Glu-42 and Lys-89 were also deleted separately. The deletion mutants (E42X and K89X) were devoid of biological activity, and the K89E mutant lost 95% of its activity. In contrast, compared with wild-type (WT) IL-18, the E42K mutant exhibited a 2-fold increase in biological activity and required a 4-fold greater concentration of IL-18BP for neutralization. The binding of WT IL-18 and its various mutants to human natural killer cells was evaluated by competition assays. The mutant E42K was more effective than WT IL-18 in inhibiting the binding of (125)I-IL-18 to natural killer cells, whereas the three inactive mutants E42X, K89E, and K89X were unable to compete with (125)I-IL-18 for binding. Similarly, WT IL-18 and the E42K mutant induced degradation of Ikappa-Balpha, whereas the three biologically inactive mutants did not induce degradation. The present study reveals that Glu-42 and Lys-89 are critical amino acid residues for the integrity of IL-18 structure and are important for binding to cell surface receptors, for signal transduction, and for neutralization by IL-18BP.
Pillars formed by laser ablation and modified by wet etching (2007)

Studies on surface texturing by chemically enhanced laser ablation in a variety of materials, particularly silicon and germanium are reported. The materials are exposed either to femtosecond or nanosecond laser irradiation in a variety of vacuum or gaseous environments including air, He, sulfur hexafluoride (SF<sub>6</sub>) or hydrogen chloride (HCl). The dynamics of pillar formation are elucidated and it is shown that the mechanisms are very different in these two pulse length regimes. Surface texturing responds to the combined effects of laser assisted chemical etching and laser ablation. Various processing steps either before or after laser irradiation allow us to modify the nature of the pillars that are formed. In this way we can make ordered arrays that extend over &#8805;1 cm<sup>2</sup> in just a few minutes of laser exposure. Post-laser processing wet etching can produce Si pillars that are over 50 &mgr;m long with tips that are only 10 nm across as well as macroporous silicon with crystallographically defined pores. A process we call solidification driven extrusion creates nanoscale spikes atop the pillars under certain circumstances - a process that is more prevalent for Ge than Si. Pillar-covered surfaces of Si and Ge are black; that is, they exhibit very low reflectivity. For Si this low reflectivity extends to wavelengths far below the band gap raising the possibility that we may be able to make other transparent materials highly absorptive by laser texturing.
Field programmable gate array based control of Dual Active Bridge DC/DC Converter for the UNIFLEX-PM project (2011)

This paper presents a Field Programmable Gate Array (FPGA) implemented control system for a Dual Active Bridge (DAB) DC/DC Converter. This implementation was required during the UNIFLEX-PM project to reduce the required computational burden on the Digital Signal Processor (DSP) used for the grid power flow control algorithms. The presented design is verified using one of the 25kVA Dual Active Bridge DC/DC Converters from the UNIFLEX-PM experimental prototype.
A statistical model for dynamic ridematching on the World Wide Web (2003)

Seattle Smart Traveler (SST) is an application of World Wide Web (WWW) technology to test the concept of automated dynamic ride-share matching. This paper reports a new statistical model for quantifying ride-share matching and car pooling. The model is validated using the SST experimental results, and the model demonstrates that the car-pooling process is a quadratic function of the number of users participating.
Prophylaxis of Posttraumatic Seizures (1990)

The issue of routine anticonvulsant prophylaxis for early and late posttraumatic epilepsy (PTE) has received much attention in the medical literature. Such problems as lack of standard definitions for early and late PTE, the retrospective design of most studies, the wide variability of inclusion and exclusion criteria, and the varied duration of follow-up make this body of literature extremely difficult to evaluate. Severe head trauma appears to cause injured neurons to become hyperexcitable; this in turn brings about the formation of an epileptogenic focus during the time between trauma and seizure occurrence. Both military and civilian head injury populations have been used to evaluate the incidence of PTE. Early seizures (i.e., less than 7 days) occur in approximately 3-5 percent of the head injury patients in both the military and civilian groups. Factors increasing this incidence include intracranial hematoma, focal neurologic deficits, posttraumatic amnesia (PTA) lasting greater than 24 hours, depressed skull fracture, and age less than 5 years. The incidence of late seizures is directly related to the extent of brain damage. The military population, composed primarily of cases with penetrating head injury, is associated with a late PTE incidence of approximately 30-50 percent. Closed head injuries in the military population involve a 5-15 percent seizure incidence. Late PTE incidence after head injuries in the civilian population is less than 5 percent. Risk factors associated with late PTE include loss of consciousness or PTA lasting greater than 24 hours, dural lacerations, depressed skull fractures, and various computerized tomography deficits. These factors vary slightly between the military and civilian populations.(ABSTRACT TRUNCATED AT 250 WORDS)
Nerve fibers sensitive to ionic taste stimuli in chorda tympani of the rat (1983)

Hypotheses about the peripheral basis for the sense of taste in mammals have been based to a considerable degree on the determined sensibilities of the nerve fibers in the chorda tympani of the rat to chemical stimulation of the anterior tongue. Yet, whether neuron types exist in this nerve, the nature of the basic mechanisms of taste reception that are tapped by this nerve and the form in which information about stimulus quality and intensity is transmitted to the central nervous system by this nerve are, at present, unresolved issues. These issues are addressed in the present study, which is a detailed analysis of the responses of rat chorda tympani nerve fibers that are sensitive to ionic stimuli; solutions applied to the anterior tongue included a range of concentrations of four chemical compounds (sucrose, sodium chloride, hydrochloric acid, and quinine hydrochloride) that represent widely different taste qualities to man or rat. Of the 44 nerve fibers sampled, 40 were stimulated most by one of the two ionic stimuli at test concentrations reported to be equally effective: 21 fibers were most responsive to 0.1 M NaCl and named N units; 19 fibers were most responsive to 0.01 M HCl and named H units. Although many N and H units responded to both HCl and NaCl, the distribution of NaCl-HCl response ratios was bimodal, indicating there are two varieties of units sensitive to ionic taste stimuli in the rat chorda tympani. Sucrose (0.5 M) affected 4 of the nerve fibers and was the most effective stimulus for 3 of them; 0.02 M quinine affected 13 of the fibers but 10 of these were H units. H units were less "specifically tuned" than N units; they were more likely to respond to several of the chemicals. Although the absolute sensitivity to NaCl in N units or to HCl in H units varied more than 10-fold, the relative effects of the four stimuli (response profiles) were generally similar for units of a given type. Exceptions occurred when H unit responses to NaCl or quinine were suppressed by prolonged effects of preceding HCl stimulation. The similarity in response profiles is reflected in high and significant correlations between responses to each pair of effective stimuli across either H or N units.(ABSTRACT TRUNCATED AT 400 WORDS)
MARTs and MARylation in the Cytosol: Biological Functions, Mechanisms of Action, and Therapeutic Potential (2021)

Mono(ADP-ribosyl)ation (MARylation) is a regulatory post-translational modification of proteins that controls their functions through a variety of mechanisms. MARylation is catalyzed by mono(ADP-ribosyl) transferase (MART) enzymes, a subclass of the poly(ADP-ribosyl) polymerase (PARP) family of enzymes. Although the role of PARPs and poly(ADP-ribosyl)ation (PARylation) in cellular pathways, such as DNA repair and transcription, is well studied, the role of MARylation and MARTs (i.e., the PARP 'monoenzymes') are not well understood. Moreover, compared to PARPs, the development of MART-targeted therapeutics is in its infancy. Recent studies are beginning to shed light on the structural features, catalytic targets, and biological functions of MARTs. The development of new technologies to study MARTs have uncovered essential roles for these enzymes in the regulation of cellular processes, such as RNA metabolism, cellular transport, focal adhesion, and stress responses. These insights have increased our understanding of the biological functions of MARTs in cancers, neuronal development, and immune responses. Furthermore, several novel inhibitors of MARTs have been developed and are nearing clinical utility. In this review, we summarize the biological functions and molecular mechanisms of MARTs and MARylation, as well as recent advances in technology that have enabled detection and inhibition of their activity. We emphasize PARP-7, which is at the forefront of the MART subfamily with respect to understanding its biological roles and the development of therapeutically useful inhibitors. Collectively, the available studies reveal a growing understanding of the biochemistry, chemical biology, physiology, and pathology of MARTs.
Detection of luminescent single ultrasmall silicon nanoparticles using fluctuation correlation spectroscopy (2000)

We dispersed electrochemical etched Si into a colloid of ultrasmall blue luminescent nanoparticles, observable with the naked eye, in room light. We use two-photon near-infrared femtosecond excitation at 780 nm to record the fluctuating time series of the luminescence, and determine the number density, brightness, and size of diffusing fluorescent particles. The luminescence efficiency of particles is high enough such that we are able to detect a single particle, in a focal volume, of 1 pcm3. The measurements yield a particle size of 1 nm, consistent with direct imaging by transmission electron microscopy. They also yield an excitation efficiency under two-photon excitation two to threefold larger than that of fluorescein. Detection of single particles paves the way for their use as labels in biosensing applications.
Scrapie-associated PrP accumulation and agent replication: effects of sulphated glycosaminoglycan analogues (1994)

An abnormally protease-resistant and apparently neuropathogenic form of PrP accumulates in the brains of hosts with scrapie and related transmissible spongiform encephalopathies. Studies with scrapie-infected neuroblastoma cells have highlighted dramatic differences in the metabolism of the normal (protease-sensitive) and scrapie-associated (protease-resistant) isoforms of PrP. Furthermore, this model has been useful in identifying inhibitors of protease-resistant PrP accumulation and scrapie agent replication which are valuable as potential therapeutic agents and as probes of the mechanism of protease-resistant PrP formation. These inhibitors include the amyloid stain Congo red and certain sulphated glycans which are glycosaminoglycans themselves or glycosaminoglycan analogues. The relative potencies of various sulphated glycans correlate with their previously determined anti-scrapie activities in vivo, suggesting that the prophylactic effects of sulphated polyanions is due to inhibition of protease-resistant PrP accumulation. These and other observations suggest that an interaction of PrP with endogenous sulphated glycosaminoglycans or proteoglycans is important in protease-resistant PrP accumulation, and raise the possibility that therapies for transmissible spongiform encephalopathies and other amyloidoses could be based on blocking (pre)amyloid-glycosaminoglycan interactions.
Effective magnetic Hamiltonian and Ginzburg criterion for fluids (1998)

We develop further the approach of Hubbard and Schofield [Phys. Lett. 40A, 245 (1972)], which maps the fluid Hamiltonian onto a magnetic one. We show that all coefficients of the resulting effective Landau-Ginzburg-Wilson (LGW) Hamiltonian may be expressed in terms of the compressibility of a reference fluid containing only repulsive interactions and its density derivatives; we calculate the first few coefficients in the case of the hard-core reference fluid. From this LGW Hamiltonian we deduce approximate mean-field relations between critical parameters and test them on data for Lennard-Jones, square-well, and hard-core Yukawa fluids. We estimate the Ginzburg criterion for these fluids.
Role of a JAK3-dependent Biochemical Signaling Pathway in Platelet Activation and Aggregation (2001)

Here we provide experimental evidence that identifies JAK3 as one of the regulators of platelet function. Treatment of platelets with thrombin induced tyrosine phosphorylation of the JAK3 target substrates STAT1 and STAT3. Platelets from JAK3-deficient mice displayed a decrease in tyrosine phosphorylation of STAT1 and STAT3. In accordance with these data, pretreatment of human platelets with the JAK3 inhibitor WHI-P131 markedly decreased the base-line enzymatic activity of constitutively active JAK3 and abolished the thrombin-induced tyrosine phosphorylation of STAT1 and STAT3. Following thrombin stimulation, WHI-P131-treated platelets did not undergo shape changes indicative of activation such as pseudopod formation. WHI-P131 inhibited thrombin-induced degranulation/serotonin release as well as platelet aggregation. Highly effective platelet inhibitory plasma concentrations of WHI-P131 were achieved in mice without toxicity. WHI-P131 prolonged the bleeding time of mice in a dose-dependent manner and improved event-free survival in a mouse model of thromboplastin-induced generalized and invariably fatal thromboembolism. To our knowledge, WHI-P131 is the first anti-thrombotic agent that prevents platelet aggregation by inhibiting JAK3.
High-Efficiency Nonfullerene Polymer Solar Cell Enabling by Integration of Film-Morphology Optimization, Donor Selection, and Interfacial Engineering (2016)

Carrier mobility is a vital factor determining the electrical performance of organic solar cells. In this paper we report that a high-efficiency nonfullerene organic solar cell (NF-OSC) with a power conversion efficiency of 6.94 ± 0.27% was obtained by optimizing the hole and electron transportations via following judicious selection of polymer donor and engineering of film-morphology and cathode interlayers: (1) a combination of solvent annealing and solvent vapor annealing optimizes the film morphology and hence both hole and electron mobilities, leading to a trade-off of fill factor and short-circuit current density (Jsc); (2) the judicious selection of polymer donor affords a higher hole and electron mobility, giving a higher Jsc; and (3) engineering the cathode interlayer affords a higher electron mobility, which leads to a significant increase in electrical current generation and ultimately the power conversion efficiency (PCE).
Fate of the mammalian cardiac neural crest (2000)

A subpopulation of neural crest termed the cardiac neural crest is required in avian embryos to initiate reorganization of the outflow tract of the developing cardiovascular system. In mammalian embryos, it has not been previously experimentally possible to study the long-term fate of this population, although there is strong inference that a similar population exists and is perturbed in a number of genetic and teratogenic contexts. We have employed a two-component genetic system based on Cre/lox recombination to label indelibly the entire mouse neural crest population at the time of its formation, and to detect it at any time thereafter. Labeled cells are detected throughout gestation and in postnatal stages in major tissues that are known or predicted to be derived from neural crest. Labeling is highly specific and highly efficient. In the region of the heart, neural-crest-derived cells surround the pharyngeal arch arteries from the time of their formation and undergo an altered distribution coincident with the reorganization of these vessels. Labeled cells populate the aorticopulmonary septum and conotruncal cushions prior to and during overt septation of the outflow tract, and surround the thymus and thyroid as these organs form. Neural-crest-derived mesenchymal cells are abundantly distributed in midgestation (E9.5-12.5), and adult derivatives of the third, fourth and sixth pharyngeal arch arteries retain a substantial contribution of labeled cells. However, the population of neural-crest-derived cells that infiltrates the conotruncus and which surrounds the noncardiac pharyngeal organs is either overgrown or selectively eliminated as development proceeds, resulting for these tissues in a modest to marginal contribution in late fetal and postnatal life.
Dryad (2007)

Dryad is a general-purpose distributed execution engine for coarse-grain data-parallel applications. A Dryad application combines computational "vertices" with communication "channels" to form a dataflow graph. Dryad runs the application by executing the vertices of this graph on a set of available computers, communicating as appropriate through flies, TCP pipes, and shared-memory FIFOs. The vertices provided by the application developer are quite simple and are usually written as sequential programs with no thread creation or locking. Concurrency arises from Dryad scheduling vertices to run simultaneously on multiple computers, or on multiple CPU cores within a computer. The application can discover the size and placement of data at run time, and modify the graph as the computation progresses to make efficient use of the available resources. Dryad is designed to scale from powerful multi-core single computers, through small clusters of computers, to data centers with thousands of computers. The Dryad execution engine handles all the difficult problems of creating a large distributed, concurrent application: scheduling the use of computers and their CPUs, recovering from communication or computer failures, and transporting data between vertices.
A 60 ns 1 Mb nonvolatile ferroelectric memory with non-driven cell plate line write/read scheme (2002)

With increase in the capacity of nonvolatile memories, the range of their use has been widening. A nonvolatile ferroelectric RAM (NVFRAM) based on a 1-transistor and 1-capacitor (1T/1C) memory cell has potential for fast-access time and small-chip size comparable with a DRAM. However, previously reported NVFRAMs are still slower than ordinary DRAMs, since driving a cell-plate line in NVFRAMs is slow. To avoid this, a non-driven cell plate line write/read scheme (NDP scheme) is presented which leads to NVFRAMs with as fast access time as DRAMs.
The manic depression of microprocessor debug (2003)

This paper describes the sometimes exhilarating, sometimes depressing, and always challenging job of leading-edge microprocessor debug. It covers an overview of processor debug, the flows, tools and methods used to perform debug, the process of "root causing" and fixing bugs, and includes case studies of actual bugs from recent processors. In conclusion, some of the future challenges for microprocessor testing are presented.
Ultrasound echo decorrelation due to acoustic radiation force (2003)

Several groups have proposed the use of acoustic radiation force as a means to characterize the mechanical properties of biological tissues. These approaches are based on the estimation of time delays between successively acquired echo lines when an internal deformation is applied. The ensemble of these delays forms a time-displacement curve that holds information about the viscoelastic response of the tissue under interrogation. The performance of such techniques is strongly dependent on the accuracy of the time delay estimates. Although noise places significant limits on the estimation process, echo decorrelation will also contribute to reduce the quality of the delay estimates. This decorrelation is similar to that observed in conventional axial elastography, even though the deformation field that results from acoustic radiation force is more complex than the one produced by axial elastography. In this paper we use analytical and computational methods to predict the decorrelation generated in acoustic radiation force imaging. We substitute derived correlation coefficients into the Cramer-Rao Lower Bound (CRLB) to predict fundamental limits on the performance of radiation force based elasticity estimation.
Isolation of cell surface-specific human monoclonal antibodies using phage display and magnetically-activated cell sorting: applications in immunohematology (1997)

A method is described for the isolation of filamentous phage-displayed human monoclonal antibodies directed at unpurifiable cell surface-expressed molecules. To optimize the capture of antigen-specific phage and minimize the binding of irrelevant phage antibodies, a simultaneous positive and negative selection strategy is employed. Cells bearing the antigen of interest are pre-coated with magnetic beads and diluted into an excess of unmodified antigen-negative cells. Following incubation of the cell admixture with a Fab/phage library, the antigen-positive cell population is retrieved using magnetically-activated cell sorting and antigen-specific Fab/phage are eluted and propagated in bacterial culture. Utilizing this protocol with magnetically-labeled Rh(D)-positive and excess unlabeled Rh(D)-negative human red blood cells and a Fab/phage library constructed from human peripheral blood lymphocytes, dozens of unique clinically-useful gamma 1 kappa and gamma 1 lambda anti-Rh(D) antibodies were isolated from a single alloimmunized individual. This cell-surface selection method is readily adaptable for use in other systems, such as for the identification of putative tumor-specific antigens and provides a rapid (< 1 month), high-yield approach for isolating self-replicative antibody reagents directed at novel or conformationally-dependent cell-surface epitopes.
Superparamagnetic Iron Oxide Nanoparticles (2004)

Superparamagnetic iron oxide (SPIO) nanoparticles are unique MR contrast agents and are of great interest for their multiple potentials. SPIO nanoparticles have a higher diagnostic accuracy for detecting metastatic lymph nodes than conventional MR studies, particularly in head and neck. The impact of this unique MR contrast agent on treatment decision of patients with head and neck cancer needs to be investigated in comparison with contrast-enhanced CT. As MR technology advances, the accuracy of SPIO nanoparticles for detection of metastasis certainly improves; thus, 1 day we may be able to reliably detect metastases in stage N0 patients, so that treatment strategy is established for each individual patient. This article presents physiologic properties of SPIO, technical considerations and diagnostic accuracy for imaging with SPIO, and other potential applications of SPIO agents.