gebhart/patrepeval huggingface dataset:
The origin and evolution of viruses (a review). (1998)

Viroids and prions might have existed early at the border of inanimate and living worlds. Most extant viruses can be characterized as derivatives of ancestors originating from episomal elements of prokaryotes (DNA phages) and later from eukaryotes. Retroviruses very likely originated from cellular retrotransposons. Retrograde evolution of some large viruses from obligatory intracellular bacteria is possible but the ontogenesis of extant bacteria does not include a viral form of existence (the filterable L forms are not viruses) and well-defined viruses do not regenerate back into vegetative bacterial forms. Biologists experimenting with the evolution of prokaryotic and eukaryotic ancient cells cannot ignore the earliest appearance of viruses within or outside the living matter. Viruses participated in and gave direction to the evolution and natural selection by coexisting with uni- and multicellular organisms for billions of years. The coevolution of viruses and their host cells is characterized by incessant attacks and counterattacks through gene rearrangements and mutations (induced in the virus by an immunological counterattack of the host or by transgression of species barriers by the virus) and recombinations. Recombinations occurred between viral and viral or viral and host genes. Acts of "molecular piracy" as practiced by ancient viruses endowed the virus with the expression of several host genes for the advantage of the virus in its replicative cycle and host-to-host spread. Probably the first immortalized and malignantly transformed cells were induced by viruses as viruses evolved anti-apoptotic measures. While infected cells resort to apoptotic death before the assembly of a new viral progeny, prominent are the anti-apoptotic measures viruses evolved in order to assure the completion of their full replicative cycle. Further, viruses may escape neutralization by host antibodies and may survive a counterattack by the host's T cells directed at virally infected cells of its own. Viruses may induce a form of tolerance and coexist with their host without inducing disease. Persistent and apparently or deceivingly apathogenic or even attenuated viral "quasi-species" populations may contain individual particles that regain virulence due to recombinations and/or gene rearrangements, especially when transgressing species barriers. Xenotropic viruses of animals may replicate in human cells and vice versa confounding experiments with xenotransplants or with use of veterinary viral vaccines for the treatment of human diseases.
A 98nW wake-up radio for wireless body area networks (2012)

A 0.13μm CMOS low power wake-up radio is presented. The wake-up radio operates with -41dBm sensitivity at 915MHz using OOK modulation with a data rate of 100kbps while consuming 98nW active power, 11pW sleep power, and has an energy efficiency of 0.98pJ/bit. The wake-up radio occupies 0.03mm <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sup> and uses two off-chip components (an inductor and a capacitor). All biasing and calibration for process variation and mismatch is included on-chip. The entire radio operates from a single 1.2V supply.
GeoPointing on indoor maps (2012)

Indoor geopointing is a mobile computing field of application where high resolution compass data is required, in order to reliably identify digital objects on a map or within a scene. When mobile application developers wish to implement geopointing applications, they are hindered by the limited accuracy and reliability of the orientation sensors that are included in today's smartphones. Calibration issues and magnetic field interference are the two major influence factors that distort the data which is generated by the compass sensor.
Protection Against Adoptive Transfer of Autoimmune Diabetes Mediated Through Very Late Antigen-4 Integrin (1994)

The very late antigen-4 (VLA-4) integrin expressed on the surface of lymphocytes and macrophages can regulate their migration to inflammatory sites as well as control cellular activation. The role of VLA-4 in the establishment of autoimmune diabetes is not easily predicted given the multiplicity of adhesion pathways and their differential use by various cell types. The contribution of VLA-4 to insulin-dependent diabetes mellitus was investigated by administration of VLA-4-specific monoclonal antibodies (MoAb) in an adoptive transfer model of disease in NOD mice. This study shows that VLA-4-specific MoAbs profoundly inhibit the development of diabetes with protection sustained by repeated MoAb exposure. Insulitis was completely inhibited during treatment and progressed to a severe degree once MoAb treatment was suspended, yet approximately 40% of treated recipients failed to become diabetic during 1-2 months post-treatment. Although we cannot rule out depletion of a relatively minor subpopulation of cells by prolonged anti-VLA-4 MoAb exposure, this inhibition of diabetes onset by treatment with MoAbs to VLA-4 supports a dependence on VLA-4 for cellular functions leading to diabetes and demonstrates that a significant disease modifying effect can be mediated by targeting the VLA-4 integrin.
<title>Sniper bullet detection by millimeter-wave radar</title> (1999)

Law enforcement and military operations would clearly benefit from a capability to locate snipers by backtracking the sniper's bullet trajectory. Achieving sufficient backtracking accuracy for bullets is a demanding radar design, requiring good measurement accuracy, high update rate, and detection of very low cross-section objects. In addition, reasonable cost is a driving requirement for law enforcement use. These divergent design requirements are addressed in an experimental millimeter-wave focal plane array radar that uses integrated millimeter-wave receiver technology. The radar is being built for DARPA by Technology Service Corporation, with assistance from M.I.T. Lincoln Laboratory and QuinStar Technology. The key element in the radar is a 35-GHz focal plane array receiver. The receiving antenna lens focuses radar signals from a wide field of view onto an array of receivers, each receiver processing a separate element of the field of view. Receiver detections are then combined in a tracking processor. An FM-CW waveform is used to provide high average power, good range resolution, and stationary clutter rejection. TSC will be testing the sniper detection radar, using radar environment simulator technology developed at Lincoln Laboratory. The simulator will retransmit the received signal with the range delay, Doppler shift, and ERP for various simulated bullet trajectories.
Participation of the major histocompatibility complex in antibody recognition of viral antigens expressed on infected cells. (1982)

The capacity of the antibody repertoire to recognize complex antigens on viral-infected cells was investigated at the level of monoclonal B cell responses. A majority of primary B cells responsive to PR8(H1N1)-infected H-2 syngeneic cells produced antibody that bound viral determinants only in the context of infected cells and not the isolated virion. An examination of the fine specificity of such antibodies revealed that most could be distinguished by a panel of cells infected with closely related heterologous H1 influenza strains. Indeed, most antibodies bound hemagglutinin determinants of PR8 exclusively, and few were broadly cross-reactive. An examination of the same antibodies for their recognition of cell surface antigens revealed that the majority recognized MHC-encoded antigenic determinants. Thus, most BALB.K (H-2k) primary B cells responsive to PR8-L919 (H-2k) cells produced monoclonal antibodies that bound PR8-antigens only in the context of H-2Dk-infected cells. Most C57BL/10 (H-2b) B cells responsive to PR8-EL4 (H-2b) cells produced monoclonal antibodies that bound PR8 antigens only in the context of H-2Kb-infected cells. These latter antibodies were further shown to recognize that H-2Kb molecule by virtue of their capacity to be discriminated by a panel of PR8-infected H-2Kb mutant cells. These findings demonstrate that much of the antibody repertoire is capable of highly specific complex recognition of viral antigenic determinants in the context of the appropriate MHC alloantigen.
Design, Synthesis, and Biophysical and Biological Evaluation of a Series of Pyrrolobenzodiazepine−Poly(N-methylpyrrole) Conjugates (2006)

A novel series of methyl ester-terminated C8-linked pyrrolobenzodiazepine (PBD)-poly(N-methylpyrrole) conjugates (50a-f) has been synthesized and their DNA interaction evaluated by thermal denaturation, DNA footprinting, and in vitro transcription stop assays. The synergistic effect of attaching a PBD unit to a polypyrrole fragment is illustrated by the large increase in DNA binding affinity (up to 50-fold) compared to the individual PBD and pyrrole components. 50a-f were found to bind mainly to identical DNA sequences but with apparent binding site widths increasing with molecular length and the majority of sites conforming to the consensus motif 5'-XGXWz (z = 3 +/- 1; W = A or T; X = any base but preferably a purine). They also provided robust sequence-selective blockade of transcription at sites corresponding approximately to their DNA footprints. 50a-f were shown to have good cellular/nuclear penetration properties, and a degree of correlation between cytotoxicity and DNA-binding affinity was observed.
The effect of polarization energy on the free energy perturbation calculations (1990)

A detailed implementation of the polarization energy and its derivatives into a molecular dynamics program is described. In order to examine the effect of the polarization energy on the calculated free energy differences, we have computed the free energy of solvation, with coordinate coupling, of normal alkanes, tetraalkylmethane, tetraalkylammonium ions and some closed shell ions in water. The pattern of the computed free energy change is compared with the results of our earlier simulations where the polarization energy was not included in the calculation. It is found that in the majority of the cases the polarization energy contribution to the free energy change is additive. The results of the simulations are also compared with the available experimental data.
Ethanol fermentation associated with solvent extraction using immobilized growing cells of Saccharomyces cerevisiae and its lactose-fermentable fusant. (1986)

An extractive fermentation for ethanol production was carried out by using immobilized cells of Saccharomyces cerevisiae Kyokai 7 and its lactose-fermentable fusant (strain PN13). Although o-isopropylphenol (OIPP) and o-tert-butylphenol (OTBP) as extractive solvents had relatively large partition coefficients against ethanol (1.4 by weight-based concentration), the solvents were heavily toxic to both yeasts. Some plant oils such as castor oil protected the yeasts from the toxicity of OTBP. Therefore, the ethanol fermentation became feasible even in the presence of OTBP as extractant by using yeast immobilized within alginate gel containing castor oil as protective agent. The ethanol production activity of gel beads containing the oil was not deteriorated through six repeated uses.
5-HT4Receptor Ligands:  Applications and New Prospects (2003)

International audience
Mechanism of attenuation of muscle protein degradation induced by tumor necrosis factor-α and angiotensin II by β-hydroxy-β-methylbutyrate (2008)

Both tumor necrosis factor-alpha (TNF-alpha)/interferon-gamma (IFN-gamma) and angiotensin II (ANG II) induced an increase in total protein degradation in murine myotubes, which was completely attenuated by treatment with beta-hydroxy-beta-methylbutyrate (HMB; 50 microM). There was an increase in formation of reactive oxygen species (ROS) within 30 min, as well as an increase in the activity of both caspase-3 and -8, and both effects were attenuated by HMB. Moreover, inhibitors of caspase-3 and -8 completely attenuated both ROS formation and total protein degradation induced by TNF-alpha/IFN-gamma and ANG II. There was an increased autophosphorylation of double-stranded RNA-dependent protein kinase (PKR), which was attenuated by the specific caspase-3 and -8 inhibitors. Neither ROS formation or protein degradation occurred in myotubes expressing a catalytically inactive PKR variant, PKRDelta6, in response to TNF-alpha/IFN-gamma, compared with myotubes expressing wild-type PKR, although there was still activation of caspase-3 and -8. HMB also attenuated activation of PKR, suggesting that it was important in protein degradation. Formation of ROS was attenuated by rotenone, an inhibitor of the mitochondrial electron transport chain, nitro-l-arginine methyl ester, an inhibitor of nitric oxide synthase, and SB 203580, a specific inhibitor of p38 mitogen-activated protein kinase (p38 MAPK), which also attenuated total protein degradation. Activation of p38 MAPK by PKR provides the link to ROS formation. These results suggest that TNF-alpha/IFN-gamma and ANG II induce muscle protein degradation by a common signaling pathway, which is attenuated by HMB, and that this involves the initial activation of caspase-3 and -8, followed by autophosphorylation and activation of PKR, which then leads to increased ROS formation via activation of p38 MAPK. Increased ROS formation is known to induce protein degradation through the ubiquitin-proteasome pathway.
Yeast Δ12 Fatty Acid Desaturase: Gene Cloning, Expression, and Function (2004)

In an effort to elucidate the molecular mechanisms of fatty acid desaturation in yeast, a complete gene encoding Delta 12 fatty acid desaturase of Saccharomyces kluyveri was cloned. The open reading frame of this gene (named Sk-FAD2) consists of 1,251 bp, encoding 416 amino acids. The deduced Sk-FAD2 protein had 37-55% identity with those from other filamentous fungi. Unlike the genes of these other fungi, S. cerevisiae expressing Sk-FAD2 was found to be capable of synthesizing the dienoic fatty acid hexadecadienoic acid as well as linoleic acid. Moreover, the Sk-FAD2-disrupted strain of S. kluyveri was unable to produce polyunsaturated fatty acids. These results suggested that Sk-FAD2 protein is a unique Delta 12 fatty acid desaturase in S. kluyveri. Analysis of transcriptional expression revealed that Sk-FAD2 was not repressed by exogenous unsaturated fatty acids but responded to low-temperature stress.
Effect of hyaluronic acid on neutrophil adhesion (1981)

The effects of hyaluronate on rabbit neutrophil adhesion were studied using a variety of techniques. Exogenous hyaluronate inhibited neutrophil aggregation under conditions of both turbulent flow and constant shear rate. Hyaluronate also inhibited neutrophil adhesion to glass. Inhibition was dose-dependent above 100 micrograms ml-1 and a minimum molecular weight for hyaluronate of 1 x 10(4) was required. These effects were not simply the result of increased bulk viscosity of the hyaluronate-containing medium, nor did they appear to be mediated by putative cell-surface receptor mechanisms. Instead, physical factors such as hindrance and/or changes in the interfacial free-energy exchange at the cell surface due to the unusual hydrodynamic properties of the hyaluronate molecule were considered to be more important. Since neutrophil migration in vivo occurs through hyaluronate-rich connective tissue matrices, the relevance of these findings for processes such as inflammation and wound healing is clear.
Insights into evolution of multicellular fungi from the assembled chromosomes of the mushroom Coprinopsis cinerea ( Coprinus cinereus ) (2010)

The mushroom Coprinopsis cinerea is a classic experimental model for multicellular development in fungi because it grows on defined media, completes its life cycle in 2 weeks, produces some 10(8) synchronized meiocytes, and can be manipulated at all stages in development by mutation and transformation. The 37-megabase genome of C. cinerea was sequenced and assembled into 13 chromosomes. Meiotic recombination rates vary greatly along the chromosomes, and retrotransposons are absent in large regions of the genome with low levels of meiotic recombination. Single-copy genes with identifiable orthologs in other basidiomycetes are predominant in low-recombination regions of the chromosome. In contrast, paralogous multicopy genes are found in the highly recombining regions, including a large family of protein kinases (FunK1) unique to multicellular fungi. Analyses of P450 and hydrophobin gene families confirmed that local gene duplications drive the expansions of paralogous copies and the expansions occur in independent lineages of Agaricomycotina fungi. Gene-expression patterns from microarrays were used to dissect the transcriptional program of dikaryon formation (mating). Several members of the FunK1 kinase family are differentially regulated during sexual morphogenesis, and coordinate regulation of adjacent duplications is rare. The genomes of C. cinerea and Laccaria bicolor, a symbiotic basidiomycete, share extensive regions of synteny. The largest syntenic blocks occur in regions with low meiotic recombination rates, no transposable elements, and tight gene spacing, where orthologous single-copy genes are overrepresented. The chromosome assembly of C. cinerea is an essential resource in understanding the evolution of multicellularity in the fungi.
Long-Term Assessment of Asenapine vs. Olanzapine in Patients with Schizophrenia or Schizoaffective Disorder (2010)

Asenapine was well tolerated over 1 year of treatment, causing less weight gain than olanzapine but more frequent extrapyramidal symptoms. PANSS total score improved with both agents; the improvement was greater with olanzapine than with asenapine using last observations carried forward but not in an observed-case analysis.
Microfibrillated cellulose, a new cellulose product: properties, uses, and commercial potential (1983)

A new form of cellulose, which is expanded to a smooth gel when dispersed in polar liquids, is produced by a unique, rapid, physical treatment of wood cellulose pulps. A 2% suspension of microfibrillated cellulose (MFC) in water has thixotropic viscosity properties and is a stable gel on storage, or when subjected to freeze-thaw cycles. At this concentration, MFC is an excellent suspending medium for other solids and an emulsifying base for organic liquids. In laboratory tests, microfibrillated cellulose has been demonstrated to have wide utility in the preparation of foods such as low-calorie whipped toppings, cake frostings, salad dressings, gravies, and sauces. At 0.3% cellulose concentration in ground meats, MFC helps retain juices during cooking. Tests were also conducted in formulating paints, emulsions, and cosmetics and in the use of MFC as a binder for nonwoven textiles and as a mineral suspending agent. From economic studies, it is estimated that a 2% MFC dispersion can be produced for about 1.5 cents/lb, total cost. 6 references, 9 figures, 2 tables.
Targeted gene disruption of murine CD7 (1997)

CD7 is a 40 kDa type I transmembrane glycoprotein member of the Ig superfamily. CD7 is a marker of mature human T cells and NK cells, and is expressed early in their development. Cross-linking CD7 positively modulates T cell and NK cell activity as measured by calcium fluxes, expression of adhesion molecules, cytokine secretion and proliferation. CD7 associates directly with phosphoinositol 3'-kinase, and CD7 ligation induces production of D-3 phosphoinositides and tyrosine phosphorylation. Severe combined immunodeficiency has been associated with a lack of lymphocyte surface CD7. The CD7 ligand is unknown. The murine CD7 homolog is encoded by a single gene on chromosome 11. In order to characterize the role of CD7 in lymphocyte development and function we have eliminated the CD7 gene by targeted disruption. CD7-deficient mice display normal histology of thymus and spleen, normal lymphocyte populations in primary and secondary lymphoid tissues, and normal serum Ig levels. Specific antibody responses after immunization with T-dependent and T-independent antigens are equivalent in wild-type and CD7 knockout mice. CD7-deficient lymphocytes respond normally to T cell mitogenic and allogeneic stimuli, and display normal NK cell cytotoxicity.
In Vitro RNA Synthesis from Exogenous Dengue Viral RNA Templates Requires Long Range Interactions between 5′- and 3′-Terminal Regions That Influence RNA Structure (2001)

Viral replicases of many positive-strand RNA viruses are membrane-bound complexes of cellular and viral proteins that include viral RNA-dependent RNA polymerase (RdRP). The in vitro RdRP assay system that utilizes cytoplasmic extracts from dengue viral-infected cells and exogenous RNA templates was developed to understand the mechanism of viral replication in vivo. Our results indicated that in vitro RNA synthesis at the 3'-untranslated region (UTR) required the presence of the 5'-terminal region (TR) and the two cyclization (CYC) motifs suggesting a functional interaction between the TRs. In this study, using a psoralen-UV cross-linking method and an in vitro RdRP assay, we analyzed structural determinants for physical and functional interactions. Exogenous RNA templates that were used in the assays contained deletion mutations in the 5'-TR and substitution mutations in the 3'-stem-loop structure including those that would disrupt the predicted pseudoknot structure. Our results indicate that there is physical interaction between the 5'-TR and 3'-UTR that requires only the CYC motifs. RNA synthesis at the 3'-UTR, however, requires long range interactions involving the 5'-UTR, CYC motifs, and the 3'-stem-loop region that includes the tertiary pseudoknot structure.
Spatial Dependency Parsing for Semi-Structured Document Information Extraction (2020)

Information Extraction (IE) for semi-structured document images is often approached as a sequence tagging problem by classifying each recognized input token into one of the IOB (Inside, Outside, and Beginning) categories. However, such problem setup has two inherent limitations that (1) it cannot easily handle complex spatial relationships and (2) it is not suitable for highly structured information, which are nevertheless frequently observed in real-world document images. To tackle these issues, we first formulate the IE task as spatial dependency parsing problem that focuses on the relationship among text tokens in the documents. Under this setup, we then propose SPADE (SPAtial DEpendency parser) that models highly complex spatial relationships and an arbitrary number of information layers in the documents in an end-to-end manner. We evaluate it on various kinds of documents such as receipts, name cards, forms, and invoices, and show that it achieves a similar or better performance compared to strong baselines including BERT-based IOB taggger.
Desmoglein-2: A Novel Regulator of Apoptosis in the Intestinal Epithelium (2007)

Intestinal epithelial intercellular junctions regulate barrier properties, and they have been linked to epithelial differentiation and programmed cell death (apoptosis). However, mechanisms regulating these processes are poorly defined. Desmosomes are critical elements of intercellular junctions; they are punctate structures made up of transmembrane desmosomal cadherins termed desmoglein-2 (Dsg2) and desmocollin-2 (Dsc2) that affiliate with the underlying intermediate filaments via linker proteins to provide mechanical strength to epithelia. In the present study, we generated an antibody, AH12.2, that recognizes Dsg2. We show that Dsg2 but not another desmosomal cadherin, Dsc2, is cleaved by cysteine proteases during the onset of intestinal epithelial cell (IEC) apoptosis. Small interfering RNA-mediated down-regulation of Dsg2 protected epithelial cells from apoptosis. Moreover, we report that a C-terminal fragment of Dsg2 regulates apoptosis and Dsg2 protein levels. Our studies highlight a novel mechanism by which Dsg2 regulates IEC apoptosis driven by cysteine proteases during physiological differentiation and inflammation.