gebhart/patrepeval huggingface dataset:
Learning Qualitative Models from Physiological Signals (1994)

. Physiological models represent a useful form of knowledge, but are both difficult and time consuming to construct by hand. Further, most physiological systems are incompletely understood. This article addresses these two issues with a system that learns qualitative models from physiological signals. The qualitative representation of models allows incomplete knowledge to be encapsulated, and is based on Kuipers&amp;apos; approach used in his QSIM algorithm. The learning algorithm allows automatic generation of such models, and is based on Coiera&amp;apos;s GENMODEL algorithm. We first show that QSIM models are efficiently PAC learnable from positive examples only, and that GENMODEL is an algorithm for efficiently constructing a QSIM model consistent with a given set of examples, if one exists. We then describe the learning system in detail, including the front-end processing and segmenting stages that transform a signal into a set of qualitative states, and GENMODEL that uses these qualitative states a...
Single Injection of a Sustained-release Prostacyclin Analog Improves Pulmonary Hypertension in Rats (2007)

We developed a new drug delivery system for prostacyclin using PLGA and ONO-1301. A single injection of ONO-1301MS resulted in sustained activity for 3 weeks, and attenuated pulmonary hypertension, partly through its antiproliferative effect on vascular smooth muscle cells via inhibition of ERK phosphorylation.
Cell‐penetrating peptides: Nanocarrier for macromolecule delivery in living cells (2010)

Novel classes and applications of cell-penetrating peptides (CPPs) are being constantly discovered since they were first identified 2 decades ago. These short cationic peptides (nanomolecules) either by covalent binding or by noncovalent binding can traverse cell membranes and deliver a variety of molecules that are unable to overcome the permeability barrier in their own capacity. The ability of the CPPs to deliver variety of macromolecules, such as oligonucleotides, therapeutic drugs, proteins, and medical imaging agents, by forming nanoparticulate carriers in a range of cells has led them to emerge as a potential tool for both macromolecule delivery application and to gain insight into the fundamentals of mechanism of cellular uptake across the plasma membrane. This review explores the recent advances, challenges, and future prospects in the field of CPP-mediated cargo delivery in mammalian and plant cells. Studies have been conducted into the peptide chemistry and stability of CPP-macromolecular complexes. Most of the CPPs have been shown to be nontoxic and do not interfere with the functionality of the macromolecules delivered across the cell membrane. The mechanism of uptake of CPP-cargo complexes and the uptake of CPPs alone across the plasma membrane remains unresolved. As the world of CPPs is rapidly advancing in both mammalian and plant system, there is a promising future for the various applications of transduction and transfection into intact cells.
Extracting geographic features from the Internet to automatically build detailed regional gazetteers (2009)

The utility of every imaginable application which incorporates a gazetteer hinges on the simple fact that the resulting system will only be as useful, complete, or accurate as the underlying gazetteer itself. A major issue confronting gazetteers utilized in systems today is that they are not complete and measures of their accuracy are largely unknown. In this paper we describe a methodology which addresses this problem by automatically generating highly complete and detailed regional gazetteers from Internet sources. We utilize information extraction and integration techniques to automatically obtain geographic features and associated footprints and feature types from freely and widely available online data which could be applied to create a gazetteer for nearly any area. We discuss the distinguishing characteristics of the generated gazetteer and extend previous work to define measures which can be used to assess the completeness and accuracy of gazetteers. Using these measures, the generated gazetteer is evaluated against the Alexandria Digital Library Gazetteer and the Los Angeles Comprehensive Bibliographic Database. Our results indicate that a gazetteer created by our methods will be at least as complete as any gazetteer currently available for certain feature classes, while falling short in others. We conclude by offering suggestions to address these shortcomings.
Role of transition metal-dioxygen complexes in catalytic oxidation. Catalysis of the oxidation of phosphines by dioxygen adducts of platinum (1977)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTRole of transition metal-dioxygen complexes in catalytic oxidation. Catalysis of the oxidation of phosphines by dioxygen adducts of platinumAyusman Sen and Jack HalpernCite this: J. Am. Chem. Soc. 1977, 99, 25, 8337–8339Publication Date (Print):December 1, 1977Publication History Published online1 May 2002Published inissue 1 December 1977https://pubs.acs.org/doi/10.1021/ja00467a046https://doi.org/10.1021/ja00467a046research-articleACS PublicationsRequest reuse permissionsArticle Views316Altmetric-Citations76LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Quantization of line spectral parameters using a trellis structure (2002)

In this article, a low bit-rate low-complexity block-based trellis quantization (BTQ) scheme is proposed for quantization of line spectral frequencies for speech coding applications. The branches in the trellis diagram correspond to the LSF difference code-words and the states correspond to quantized LSF parameters. An efficient algorithm for the index generation (finding the index of a path in the trellis) is introduced. The proposed BTQ achieves the transparent coding quality at 23 bits/frame (1150 b/sec.) and offers a gain of 3 b/frame (150 b/s) and significant reduction in complexity, compared to the IS-641 split-VQ. An interframe BTQ scheme is also presented to exploit the redundancies between the adjacent frames. The interframe scheme is found to achieve an additional 50 b/sec reduction of the bit-rate and is based on adaptive block-based trellis quantization of the prediction residues.
Breaking the histone code with quantitative mass spectrometry (2011)

Histone post-translational modifications (PTMs) comprise one of the most intricate nuclear signaling networks that govern gene expression in a long-term and dynamic fashion. These PTMs are considered to be 'epigenetic' or heritable from one cell generation to the next and help establish genomic expression patterns. While much of the analyses of histones have historically been performed using site-specific antibodies, these methods are replete with technical obstacles (i.e., cross-reactivity and epitope occlusion). Mass spectrometry-based proteomics has begun to play a significant role in the interrogation of histone PTMs, revealing many new aspects of these modifications that cannot be easily determined with standard biological approaches. Here, we review the accomplishments of mass spectrometry in the histone field, and outline the future roadblocks that must be overcome for mass spectrometry-based proteomics to become the method of choice for chromatin biologists.
HB-EGF/HER-1 signaling in bone marrow mesenchymal stem cells: inducing cell expansion and reversibly preventing multilineage differentiation (2005)

Epidermal growth factor receptor-1 (EGFR-1/HER-1/ErbB-1) regulates proliferation and cell fate during epidermal development. HER-1 is activated by several EGF-family ligands including heparin-binding epidermal growth factor-like growth factor (HB-EGF), a mitogenic and chemotactic molecule that participates in tissue repair, tumor growth, and other tissue-modeling phenomena, such as angiogenesis and fibrogenesis. We found that mesenchymal stem cells (MSCs), the precursors of different mesenchymal tissues with a role in processes in which HB-EGF is often involved, normally express HER-1, but not HB-EGF itself. Under the effect of HB-EGF, MSCs proliferate more rapidly and persistently, without undergoing spontaneous differentiation. This effect occurs in a dose-dependent fashion, and is specific, direct, and HER-1 mediated, as it is inhibited by anti-HER-1 and anti-HB-EGF blocking antibodies. Moreover, HB-EGF reversibly prevents adipogenic, osteogenic, and chondrogenic differentiation induced with specific media. These data show that HB-EGF/HER-1 signaling is relevant to MSC biology, by regulating both proliferation and differentiation.
B lymphocyte precursors and myeloid progenitors survive in diffusion chamber cultures but B cell differentiation requires close association with stromal cells (1987)

The aim of this study was to investigate the relative contribution of direct contact with stromal cells v stromal cell-derived soluble mediators to the differentiation of B lymphocytes and cells from other hematopoietic lineages. This was investigated by making a comparison between hemopoietic cells grown in direct contact with stroma to those in diffusion chambers (DCs) placed over purified populations of stroma. The source of stromal cells was adherent layers from myeloid or lymphoid long-term bone marrow cultures that had been treated with mycophenolic acid, an antibiotic that depletes hemopoietic cells from the cultures but retains a functional stroma. The cells seeded into the chambers were fresh marrow cells that had been passed through two consecutive nylon wool columns to deplete cell populations capable of forming an adherent cell layer in vitro. DCs were placed in wells in which the adherent stroma, growing under myeloid or lymphoid conditions, was present. The results indicate that progenitors of granulocytes and macrophages survived and differentiated in DCs under myeloid culture conditions, as the number of cells and absolute number of CFU-GM increased over that present in the reseed population. These levels, however, were markedly less than in parallel cultures in which the cells were seeded directly onto stroma. Hematopoiesis in DCs placed over hemopoietically active stroma was not optimal, suggesting that factors were used by those hemopoietic cells closest to the stroma. A B lymphocyte precursor survived in DCs under myeloid but not lymphoid conditions, and its differentiation into B lymphocytes was dependent on close association with stromal cells; B lymphopoiesis initiated when cells from DCs grown under myeloid conditions were harvested from the chambers and seeded directly onto stroma initiated and maintained under lymphoid bone marrow culture conditions. B lymphopoiesis did not initiate if the DC from the myeloid conditions was left intact and placed directly over a lymphoid stromal cell layer in lymphoid conditions.
Systematic Survey for Novel Types of Prokaryotic Retroelements Based on Gene Neighborhood and Protein Architecture (2008)

Retroelements, elements encoding reverse transcriptase (RT), are ubiquitous in eukaryotes and have a great influence on the evolution of our genome. Detailed information is available on eukaryotic retroelements; however, prokaryotic retroelements are poorly understood. Recently, new types of eukaryotic retroelements were characterized on the basis of their gene composition and their phylogenetic positions. Here we performed a systematic survey to identify novel types of prokaryotic retroelements by analyzing gene neighborhood and protein architecture. We found novel types of gene combination and examined whether they represent actual retroelements. Five monophyletic groups were identified that were distinct from characterized prokaryotic retroelements, showed specific gene combination, were distributed patchily, and included at least 1 example of recent integration. These results strongly indicated the frequent horizontal transfer of these elements. One group encoded DNA polymerase A. A possible function of DNA polymerase A in the life cycle of retroelements is catalyzing second-strand cDNA synthesis, which is DNA polymerization performed using a DNA template not an RNA template. Another group encoded both bacterial primase and carbon-nitrogen hydrolase. Primase is likely to synthesize primers to initiate reverse transcription. Two other groups also encoded carbon-nitrogen hydrolase as a fusion protein with RT. It is difficult to speculate on the function of hydrolase in the life cycle of retroelements. The last group encoded dual RT proteins, which are likely to form heterodimers during replication. The protein sets of these 5 groups of prokaryotic retroelements were completely different from those of eukaryotic retroelements, indicating that the survival constraints of prokaryotic elements were distinct from those of eukaryotic elements. It is likely that these prokaryotic retroelements are maintained as extrachromosomal DNA or RNA or are accidentally integrated into genomes. Our findings presented the possibility that many types of extrachromosomal prokaryotic retroelements remain to be characterized. In addition, we found 8 RT genes were associated with clustered regularly interspaced short palindrome repeats (CRISPRs) of the CRISPR-Cas system. These RT genes are likely to work in immunity against RNA phages via cDNA synthesis.
Efficacy of Intralesionaliy Administered Cisplatin-impregnated Biodegradable Polymer for the Treatment of 9L Gliosarcoma in the Rat (1996)

The local instillation of cisplatin-impregnated biodegradable polymer, allowing the sustained release of high-dose chemotherapy locally, seems to be effective treatment for intracranial 9L gliosarcoma in the rat. Treatment was superior to intralesionally administered free or systemic cisplatin.
IL-17: prototype member of an emerging cytokine family (2002)

IL-17 is a potent proinflammatory cytokine produced by activated memory T cells. The large-scale sequencing of the human and other vertebrate genomes has revealed the presence of additional genes encoding proteins clearly related to IL-17, thus defining a new family of cytokines. There are at least six members of the IL-17 family in humans and in mice. Initial characterization suggests that like IL-17, several of these newly identified molecules have the ability to modulate immune function. Neither the IL-17 family nor the cognate receptors that have been identified for these molecules bear obvious sequence similarity to other known families of proteins. Thus, they represent a distinct signaling system that appears to have been highly conserved across vertebrate evolution. The potent inflammatory actions that have been identified for several of these factors and the emerging associations with major human diseases suggest that these proteins may have significant roles in inflammatory processes.
Genetic Impacts of Using Female-Sorted Semen in Commercial and Nucleus Herds (2007)

This study was designed to investigate the genetic effects of using sorted semen in a dairy cattle population. Progress was monitored in elite and commercial animals over 20 yr of selection. To study the genetic impact of using sorted semen in commercial herds, a scenario was evaluated in which female-sorted semen was available to commercial herds. Second, to study the genetic impact of using sorted semen in nucleus herds, scenarios were simulated in which female-sorted semen was used only in a centralized nucleus herd, in which multiple ovulation and embryo transfer (MOET) took place. Because of the additional advantage of marker-assisted selection when sorted semen was used in nucleus herds, a second scenario was simulated in which both sorted semen and marker-assisted selection were implemented. In the scenario in which female-sorted semen was used in commercial herds, a large genetic advantage was observed early in commercial cows. The average superiority in first-lactation cows exceeded 30% in yr 11, relative to a base scheme with regular semen, but continued to decrease until it reached 9% in yr 20. The increased selection intensity in commercial cows contributed to the genetic merit of future cows (cow-to-cow contribution), but the contribution of the nucleus grew over time and gradually marginalized the cow-to-cow contribution. The genetic advantage of gender control in MOET schemes was minimal except when marker-assisted selection was also available. Two factors that affected the contribution of marker-assisted selection were studied: 1) within- vs. across-family selection of donors, and 2) the number of loci in the quantitative trait locus component. Schemes that selected donors regardless of their family structure were superior, and the quantitative trait locus component with more loci increased the effectiveness of sorted semen. Finally, we studied a reduced MOET scheme in which the number of harvested females was reduced from 42 to 25/yr. The reduced scheme in combination with female-sorted semen was not found to be genetically inferior to the large scheme in combination with regular semen.
Multifunctional Antibodies by the Dock-and-Lock Method for Improved Cancer Imaging and Therapy by Pretargeting (2007)

The Dock-and-Lock (DNL) method, which makes bioactive molecules with multivalency and multifunctionality, is a new approach to develop targeting molecules for improved cancer imaging and therapy. It involves the use of a pair of distinct protein domains involved in the natural association between cyclic adenosine monophosphate (cAMP)-dependent protein kinase A (PKA) and A-kinase anchoring proteins (AKAPs). The dimerization and docking domain found in the regulatory subunit of PKA and the anchoring domain (AD) of an interactive AKAP are each attached to a biologic entity, and the resulting derivatives, when combined, readily form a stably tethered complex of a defined composition that fully retains the functions of the individual constituents. The DNL method has generated several trivalent, bispecific, binding proteins, each consisting of 2 identical Fab fragments linked site-specifically to a different Fab fragment. For example, 2 identical Fabs reacting with carcinoembryonic antigen (CEA) are bound to a Fab reacting with a hapten peptide that bears a diagnostic or therapeutic radionuclide. Using a 2-step, pretargeting method that separates the bivalent anti-CEA antibody targeting of tumor from the delivery of the radioactive peptide that is captured by the second Fab of the tri-Fab construct, an improved method of cancer imaging and therapy has been developed and shows very sensitive and specific targeting of CEA-expressing tumors for either diagnostic imaging, such as with immunoSPECT and immunoPET, or radioimmunotherapy. Improved therapeutic efficacy is shown with pretargeting in a pancreatic cancer xenograft model given a tri-Fab to a pancreatic cancer MUC1 and the hapten peptide labeled with (90)Y.
A Basis for Secure Communication in Large Distributed Systems (1987)

We propose a secure communication architecture for distributed systems that puts security below the transport level, and uses host-to-host rather than process-to-process secure channels. We argue that this provides the same level of end-to-end security as putting security at higher levels, and that it can simplify and improve the performance of transport protocols. The architecture is designed for very large distributed systems, which in general have security requirements beyond those of LAN-based systems.
RhoGDI deficiency induces constitutive activation of Rho GTPases and COX-2 pathways in association with breast cancer progression (2015)

Rho GDP Dissociation Inhibitor (RhoGDI) is a key regulator of Rho GTPases. Here we report that loss of RhoGDI significantly accelerated xenograft tumor growth of MDA-MB-231 cells in animal models. At the molecular level, RhoGDI depletion resulted in constitutive activation of Rho GTPases, including RhoA, Cdc42, and Rac1. This was accompanied by Rho GTPase translocation from the cytosol to membrane compartments. Notably, COX-2 protein levels, mRNA expression, and biological activity were markedly increased in RhoGDI-deficient cells. The upregulated expression of COX-2 was directly associated with increased Rho GTPase activity. Further, we assessed the expression level of RhoGDI protein in breast tumor specimens (n = 165) by immunohistochemistry. We found that RhoGDI expression is higher in the early stages of breast cancer followed by a significant decrease in malignant tumors and metastatic lesions (p < 0.01). These data suggest that downregulation of RhoGDI could be a critical mechanism of breast tumor development, which may involve the hyperactivation of Rho GTPases and upregulation of COX-2 activity. Additional studies are warranted to evaluate the therapeutic potential of inhibiting Rho GTPases and COX-2 for treating breast cancers.
Identification of K-ras as the major regulator for cytokine-dependent Akt activation in erythroid progenitors in vivo (2005)

Despite intensive investigation, controversial results have been obtained concerning the precise signaling pathway(s) regulated by K-ras in different cell types. We show that in primary fetal liver erythroid progenitors, erythropoietin activates all three Ras isoforms, but preferentially N- and K-ras. In K-ras(-/-) fetal liver cells (FLC), erythropoietin- or stem cell factor-dependent Akt activation is greatly reduced, whereas other pathways including Stat5 and p44/p42 MAP kinase are activated normally. We further studied the effects of reduced cytokine-dependent Akt activation in erythroid differentiation. We find that freshly isolated K-ras(-/-) FLC show an approximately 7-fold increase of apoptosis and delayed erythroid differentiation, but only at the stage of erythroid progenitors and very early erythroblasts. When K-ras(-/-) erythroid progenitors are cultured in vitro, there is a significant delay in erythroid differentiation but little increase in apoptosis. Furthermore, we show that partial pharmacologic inhibition of the phosphatidylinositol 3-kinase/Akt pathway in wild-type erythroid progenitors leads to a delay in erythroid differentiation similar to that observed in K-ras(-/-) FLC. Taken together, our data identify K-ras as the major regulator for cytokine-dependent Akt activation, which is important for erythroid differentiation in vivo.
High‐Performance Planar Perovskite Optoelectronic Devices: A Morphological and Interfacial Control by Polar Solvent Treatment (2015)

Highly efficient planar perovskite optoelectronic devices are realized by amine-based solvent treatment on compact TiO2 and by optimizing the morphology of the perovskite layers. Amine-based solvent treatment between the TiO2 and the perovskite layers enhances electron injection and extraction and reduces the recombination of photogenerated charges at the interface.