gebhart/patrepeval huggingface dataset:
Connexion by Boeing/sup SM/-broadband satellite communication system for mobile platforms (2002)

The Connexion by Boeing/sup SM/ will provide broadband data services and live TV to aircraft and other mobile platforms using leased Ku-band satellite transponders. System capacity and coverage will grow with market demand by leasing additional transponders. The forward link to the aircraft provides 20-40 Mbps of shared capacity. Mobile platforms may transmit at up to 1.5 Mbps on the return link. Multiple platforms typically share each return link transponder. The aggregate adjacent satellite interference produced by all platforms simultaneously sharing a transponder is strictly controlled to be below the level of interference produced by a single VSAT terminal. CONUS service uses Boeing phased array antennas.
NSs Protein of Rift Valley Fever Virus Induces the Specific Degradation of the Double-Stranded RNA-Dependent Protein Kinase (2009)

Rift Valley fever virus (RVFV) continues to cause large outbreaks of acute febrile and often fatal illness among humans and domesticated animals in Africa, Saudi Arabia, and Yemen. The high pathogenicity of this bunyavirus is mainly due to the viral protein NSs, which was shown to prevent transcriptional induction of the antivirally active type I interferons (alpha/beta interferon [IFN-alpha/beta]). Viruses lacking the NSs gene induce synthesis of IFNs and are therefore attenuated, whereas the noninducing wild-type RVFV strains can only be inhibited by pretreatment with IFN. We demonstrate here in vitro and in vivo that a substantial part of the antiviral activity of IFN against RVFV is due to a double-stranded RNA-dependent protein kinase (PKR). PKR-mediated virus inhibition, however, was much more pronounced for the strain Clone 13 with NSs deleted than for the NSs-expressing strain ZH548. In vivo, Clone 13 was nonpathogenic for wild-type (wt) mice but could regain pathogenicity if mice lacked the PKR gene. ZH548, in contrast, killed both wt and PKR knockout mice indiscriminately. ZH548 was largely resistant to the antiviral properties of PKR because RVFV NSs triggered the specific degradation of PKR via the proteasome. The NSs proteins of the related but less virulent sandfly fever Sicilian virus and La Crosse virus, in contrast, had no such anti-PKR activity despite being efficient suppressors of IFN induction. Our data suggest that RVFV NSs has gained an additional anti-IFN function that may explain the extraordinary pathogenicity of this virus.
Magneto-optical recording on patterned substrates (invited) (1996)

Patterning of glass or plastic substrates in the form of shallow square patches is a promising method of increasing the storage density for magneto-optical disks. The sidewalls of the patches pin the reverse-magnetized domains that develop in these samples. Confinement of domains within the patch boundaries during thermomagnetic recording has also been demonstrated. We have measured polarization conversion of the incident light on the sidewalls of the patches; a method to reduce the amount of such polarization conversion is proposed in this article.
13 Splicing of Precursors to mRNA by the Spliceosome (1993)

I. INTRODUCTION The RNA world pictures a time when RNA structures catalyzed many reactions, almost certainly including RNA splicing. The self-splicing reactions of group I and group II introns may be direct remnants of the RNA world. Both of these catalytic structures can facilitate cis -splicing, where the two exons are initially part of a contiguous RNA, and trans -splicing, where the two exons are initially on two separate RNAs. In the latter case, the partial intron sequences flanking the two exons pair through sequence complementarity to form a catalytic structure joining the associated exons. Many have speculated that the exon-intron structure was common in the genetic material in the RNA world. In fact, exons have been hypothesized as having originally evolved as units of sequences which encoded functional protein domains that were assembled by RNA splicing into large multidomain proteins with more complex functions. In this period, it is highly likely that RNA splicing was the product of the action of group I- and group II-like catalytic structures, and peptide-bond formation was catalyzed by progenitors of ribosomal RNA. As the potential to generate specific proteins evolved, some of these proteins probably bound to sequences within the catalytic introns to facilitate the rate of splicing. Eventually, the situation must have evolved to a stage where a fragment of RNA derived from a catalytic group I- or group II-like intron was transcribed in abundance and began to associate in trans with many different self-splicing introns to facilitate splicing. Perhaps the RNA fragment promoted...
Molecular Mechanism of Oxygen Isotopic Exchange over Supported Vanadium Oxide Catalyst VOx/TiO2 (2013)

Detailed molecular mechanisms of oxygen isotopic exchange over VOx/TiO2 catalyst following the R0, R1, and R2 mechanisms were studied using periodic DFT analysis of possible pathways by the CI-NEB method. The electronic structures of surface VOx species formed on the VOx/TiO2 model surface after interaction of molecular oxygen with fully oxidized O═V5+–O–V5+═O sites and reduced V3+–O–V3+ sites were analyzed. We found a number of metastable surface structures that are potential intermediates in the exchange reaction pathways. We present evidence that adsorption of two gas-phase oxygen molecules on a reduced V3+–O-V3+ site leads to the formation of a superoxide complex, followed by its transformation into a peroxide complex with low activation energy about E* = 0.04 eV (0.92 kcal/mol). Subsequent transformation of this surface superoxide-peroxide species follows the Langmuir–Hinshelwood mechanism without participation of lattice oxygen along the R0 reaction pathway. We demonstrate that adsorption of molecular oxygen on fully oxidized O═V5+–O–V5+═O sites results in the formation of either monodentate V<(O3) or bidentate V<(O3)>V surface ozonide species. Their subsequent transformations result in oxygen isotopic exchange following the R1 or R2 mechanisms with the activation energies in the range of 1.44 to 1.64 eV for the R1 mechanism and 1.81 eV for the R2 one. These processes follow the Eley–Rideal mechanism with participation of one or two lattice oxygen atoms, correspondingly.
A ligand-free solid-supported system for Sonogashira couplings: applications in nucleoside chemistry (2005)

A mild heterogeneous, ligand-free protocol for Sonogashira and Heck couplings has been developed and used to access several biologically important deoxynucleoside derivatives in a facile manner.
Exposure of cartilage to a fibronectin fragment amplifies catabolic processes while also enhancing anabolic processes to limit damage (1998)

The addition of fibronectin fragments to cultured cartilage causes an initial suppression of proteoglycan synthesis, induction of matrix metalloproteinases, and resultant decrease in proteoglycan content by about 50% during the first few days in culture. Because the proteoglycan loss appears to be limited, we investigated whether the fibronectin fragments induce anabolic responses that might counter the damage. The effects of various lengths of exposure of cultured cartilage to the fibronectin fragment on proteoglycan content, proteoglycan synthesis rates, stromelysin-1 release, and tumor necrosis factor-alpha, interleukin-1alpha, and interleukin-6 release were investigated. The results showed that about 7 days of exposure of cultured cartilage to the fibronectin fragment was required for maximal cytokine release, proteoglycan depletion, and stromelysin-1 release. However, nearly maximal suppression of proteoglycan synthesis occurred within 1 day of the addition of the fibronectin fragment and, after its removal, the rates increased to supernormal levels. Decreasing exposure to 3 days caused only a small decrease in cartilage proteoglycan content, although stromelysin-1 release still occurred. Decreasing exposure to 1 day caused an immediate increase in proteoglycan synthesis and an increase to supernormal proteoglycan contents. The effect of first treating cartilage with the fibronectin fragment for various periods and then allowing a recovery was to make the cartilage more resistant to secondary exposures. This study shows that cartilage damage can be caused by short exposures to the fibronectin fragment and that exposures either optimal or suboptimal for damage additionally amplify anabolic processes to make the cartilage resistant to further damage and, thus, condition it against pending amplification of damage.
Antibiotic‐induced SOS response promotes horizontal dissemination of pathogenicity island‐encoded virulence factors in staphylococci (2005)

Although mobile genetic elements have a crucial role in spreading pathogenicity-determining genes among bacterial populations, environmental and genetic factors involved in the horizontal transfer of these genes are largely unknown. Here we show that SaPIbov1, a Staphylococcus aureus pathogenicity island that belongs to the growing family of these elements that are found in many strains, is induced to excise and replicate after SOS induction of at least three different temperate phages, 80alpha, phi11 and phi147, and is then packaged into phage-like particles and transferred at high frequency. SOS induction by commonly used fluoroquinolone antibiotics, such as ciprofloxacin, also results in replication and high-frequency transfer of this element, as well as of SaPI1, the prototypical island of S. aureus, suggesting that such antibiotics may have the unintended consequence of promoting the spread of bacterial virulence factors. Although the strains containing these prophages do not normally contain SaPIs, we have found that RF122-1, the original SaPIbov1-containing clinical isolate, contains a putative second pathogenicity island that is replicated after SOS induction, by antibiotic treatment, of the prophage(s) present in the strain. Although SaPIbov1 is not induced to replicate after SOS induction in this strain, it is transferred by the antibiotic-activated phages. We conclude that SOS induction by therapeutic agents can promote the spread of staphylococcal virulence genes.
Primary myelofibrosis: 2012 update on diagnosis, risk stratification, and management (2011)

Observation alone is adequate for asymptomatic low/intermediate-1 risk disease. Allogeneic stem cell transplantation or experimental drug therapy is considered for intermediate-2/ high risk disease. Conventional or experimental drug therapy is reasonable for symptomatic intermediate-1 risk disease. Splenectomy and low-dose radiotherapy are used for drug-refractory splenomegaly. Radiotherapy is also used for the treatment of non-hepatosplenic EMH, PMF-associated pulmonary hypertension, and extremity bone pain.
A threading-based method (FINDSITE) for ligand-binding site prediction and functional annotation (2007)

The detection of ligand-binding sites is often the starting point for protein function identification and drug discovery. Because of inaccuracies in predicted protein structures, extant binding pocket-detection methods are limited to experimentally solved structures. Here, FINDSITE, a method for ligand-binding site prediction and functional annotation based on binding-site similarity across groups of weakly homologous template structures identified from threading, is described. For crystal structures, considering a cutoff distance of 4 A as the hit criterion, the success rate is 70.9% for identifying the best of top five predicted ligand-binding sites with a ranking accuracy of 76.0%. Both high prediction accuracy and ability to correctly rank identified binding sites are sustained when approximate protein models (<35% sequence identity to the closest template structure) are used, showing a 67.3% success rate with 75.5% ranking accuracy. In practice, FINDSITE tolerates structural inaccuracies in protein models up to a rmsd from the crystal structure of 8-10 A. This is because analysis of weakly homologous protein models reveals that about half have a rmsd from the native binding site <2 A. Furthermore, the chemical properties of template-bound ligands can be used to select ligand templates associated with the binding site. In most cases, FINDSITE can accurately assign a molecular function to the protein model.
Effects of High-Dose IFNα2b on Regional Lymph Node Metastases of Human Melanoma: Modulation of STAT5, FOXP3, and IL-17 (2008)

IFNalpha2b up-regulates STAT5 and down-regulates STAT3, in conjunction with up-regulation of Treg and inhibition of IL-17-expressing lymphocytes in melanoma tissues. These findings suggest that the effects of IFNalpha may be potentiated through interference with the response of Tregs and/or STAT5.
Pathobiology of pulmonary fibrosis (1990)

Pulmonary fibrosis is characterized by an increase in lung matrix and alterations in the numbers and spatial relationships of lung parenchymal cells. The increase in matrix results from a proliferation and "activation" of fibroblasts (FB) with increased production and deposition of matrix macromolecules at sites of lung injury. Connective tissue cell activation is associated with increased gene expression of collagens, fibronectin, proteoglycans and other matrix components; cytoskeletal alterations; and probably also with changes in the expression of matrix receptors and matrix-degrading enzymes and inhibitors. The fibroproliferative reaction involves the participation of a variety of cytokines and inflammatory mediators by resident and inflammatory cells at sites of lung injury. Thickening of the alveolar wall can result secondary to matrix deposition within the interstitium and as a result of "mural incorporation" of organized airspace exudate. However, marked structural remodeling of the gas-exchange tissues, with the development of honeycomb lung, involves airspace fibrosis and alveolar collapse. The latter processes lead to areas of airspace obliteration secondary to airspace filling, and to fibrous adhesion of collapsed septa. The extent of airspace obliteration is determined largely by the severity or extent of epithelial injury. Although lung fibrosis is usually irreversible, the activated state is reversible after clearance of exudate and reepithelialization. A continuing and seemingly autonomous fibroproliferative reaction can result in the face of ongoing injury and delayed repair.
The Combined Tool Approach for Face Mask Removal During On-field Conditions (2008)

Combining the cordless screwdriver and cutting tool provided a fast and reliable means of on-field FM removal in this Division II setting. Despite the excellent overall result, 1 FM was not removed in a timely manner. Therefore, we recommend that athletic trainers practice helmet removal to be prepared should FM removal fail.
RAPID BIOMOLECULE ANALYSIS USING TWO-DIMENSIONAL ELECTROPHORESIS-ELECTROSPRAY IONIZATION MICROCHIP (2011)

We demonstrate a two-dimensiona l (2D) separation microchip allowing capillary isoelectric focusing-capillary zone electrophoresis (cIEF-CZE) to be coupled to electrospray ionization mass spectrometry (ESI/MS). In the first dimension, separation is according to pI values (cIEF), while CZE occurs in the second dimension during mobilization towards the monolithically integrated ESI emitter. The setup results in shorter analysis times (cIEF 100 s and CZE 53.6-75.4 s) than that of conventional cIEF as well as in improved resolving power and better selectivity than those of microchip cIEF or CZE alone.
Genetic Variations and Polymorphisms of G Protein-Coupled Receptors: Functional and Therapeutic Implications (2001)

G protein-coupled receptors (GPCRs) represent a major class of proteins in the genome of many species, including humans. In addition to the mapping of a number of human disorders to regions of the genome containing GPCRs, a growing body of literature has documented frequently occurring variations (i.e. polymorphisms) in GPCR loci. In this article, we use a domain-based approach to systematically examine examples of genetic variation in the coding and noncoding regions of GPCR loci. Data to date indicate that residues in GPCRs are involved in ligand binding and coupling to G proteins and that regulation can be altered by polymorphisms. Studies of GPCR polymorphisms have also uncovered the functional importance of residues not previously implicated from other approaches that are involved in the function of GPCRs. We predict that studies of GPCR polymorphisms will have a significant impact on medicine and pharmacology, in particular, by providing new means to subclassify patients in terms of both diagnosis and treatment.
Long stretches of short tandem repeats are present in the largest replicons of the Archaea Haloferax mediterranei and Haloferax volcanii and could be involved in replicon partitioning (1995)

We report the presence of long stretches of tandem repeats in the genome of the halophilic Archaea Haloferax mediterranei and Haloferax volcanii. A 30 bp sequence with dyad symmetry (including 5 bp inverted repeats) was repeated in tandem, interspersed with 33-39 bp unique sequences. This structure extends for long stretches--1.4 kb at one location in H. mediterranei chromosome and about 3 kb in the H. volcanii chromosome. The tandem repeats (designated TREPs) show a similar distribution in both organisms, appearing once or twice in the H. volcanii and H. mediterranei chromosomes, and once in the largest, probably essential megaplasmid of each organism but not in the smaller replicons. Sequencing of the structures in both H. volcanii replicons revealed an extremely high sequence conservation in both replicons within the species, as well as in the different organisms. Homologous sequences have also been found in other more distantly related halophilic members of the Archaea. Transformation of H. volcanii with a recombinant plasmid containing a 1.1 kb fragment of the TREPs produced significant alterations in the host cells, particularly in terms of cell viability. The introduction of extra copies of TREPs within the vector significantly alters the distribution of the genome among the daughter cells, as observed by DAPI staining. Although the precise biological role cannot be completely ascertained, all the data conform with the tandem repeats being involved in replicon partitioning in halobacteria.
Consistent bipartite graph co-partitioning for star-structured high-order heterogeneous data co-clustering (2005)

Heterogeneous data co-clustering has attracted more and more attention in recent years due to its high impact on various applications. While the co-clustering algorithms for two types of heterogeneous data (denoted by pair-wise co-clustering), such as documents and terms, have been well studied in the literature, the work on more types of heterogeneous data (denoted by high-order co-clustering) is still very limited. As an attempt in this direction, in this paper, we worked on a specific case of high-order co-clustering in which there is a central type of objects that connects the other types so as to form a star structure of the inter-relationships. Actually, this case could be a very good abstract for many real-world applications, such as the co-clustering of categories, documents and terms in text mining. In our philosophy, we treated such kind of problems as the fusion of multiple pair-wise co-clustering sub-problems with the constraint of the star structure. Accordingly, we proposed the concept of consistent bipartite graph co-partitioning, and developed an algorithm based on semi-definite programming (SDP) for efficient computation of the clustering results. Experiments on toy problems and real data both verified the effectiveness of our proposed method.
Sialyl Lewis X mimics derived from a pharmacophore search are selectin inhibitors with anti-inflammatory activity. (1994)

The selectins, a family of adhesion receptors involved in leukocyte extravasation, recognize sialyl Lewis X (sLe(x); NeuAc alpha 2-3Gal beta 1-4(Fuc alpha 1-3)GlcNAc) and related oligosaccharides. We used conformational energy computations, high field NMR, and structure-function studies to define distance parameters of critical functional groups of sLe(x). This sLe(x) pharmacophore was used to search a three-dimensional data base of chemical structures. Compounds that had a similar spatial relationship of functional groups were tested as inhibitors of selectin binding. Glycyrrhizin, a triterpene glycoside, was identified and found to block selectin binding to sLe(x) in vitro. We substituted different sugars for the glucuronic acids of glycyrrhizin and found the L-fucose derivative to be the most active in vitro and in vivo. A C-fucoside derivative, synthesized on a linker designed for stability and to more closely approximate the original sLe(x) pharmacophore, resulted in an easily synthesized, effective selectin blocker with anti-inflammatory activity.
A pitch extraction algorithm tuned for automatic speech recognition (2014)

In this paper we present an algorithm that produces pitch and probability-of-voicing estimates for use as features in automatic speech recognition systems. These features give large performance improvements on tonal languages for ASR systems, and even substantial improvements for non-tonal languages. Our method, which we are calling the Kaldi pitch tracker (because we are adding it to the Kaldi ASR toolkit), is a highly modified version of the getf0 (RAPT) algorithm. Unlike the original getf0 we do not make a hard decision whether any given frame is voiced or unvoiced; instead, we assign a pitch even to unvoiced frames while constraining the pitch trajectory to be continuous. Our algorithm also produces a quantity that can be used as a probability of voicing measure; it is based on the normalized autocorrelation measure that our pitch extractor uses. We present results on data from various languages in the BABEL project, and show a large improvement over systems without tonal features and systems where pitch and POV information was obtained from SAcC or getf0.
Spatial Compressive Sensing for MIMO Radar (2013)

We study compressive sensing in the spatial domain to achieve target localization, specifically direction of arrival (DOA), using multiple-input multiple-output (MIMO) radar. A sparse localization framework is proposed for a MIMO array in which transmit and receive elements are placed at random. This allows for a dramatic reduction in the number of elements needed, while still attaining performance comparable to that of a filled (Nyquist) array. By leveraging properties of structured random matrices, we develop a bound on the coherence of the resulting measurement matrix, and obtain conditions under which the measurement matrix satisfies the so-called isotropy property. The coherence and isotropy concepts are used to establish uniform and non-uniform recovery guarantees within the proposed spatial compressive sensing framework. In particular, we show that non-uniform recovery is guaranteed if the product of the number of transmit and receive elements, MN (which is also the number of degrees of freedom), scales with K(logG) <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> , where K is the number of targets and G is proportional to the array aperture and determines the angle resolution. In contrast with a filled virtual MIMO array where the product MN scales linearly with G, the logarithmic dependence on G in the proposed framework supports the high-resolution provided by the virtual array aperture while using a small number of MIMO radar elements. In the numerical results we show that, in the proposed framework, compressive sensing recovery algorithms are capable of better performance than classical methods, such as beamforming and MUSIC.