gebhart/patrepeval huggingface dataset:
Enhanced Yield of Neuroepithelial Precursors and Midbrain-Like Dopaminergic Neurons from Human Embryonic Stem Cells Using the Bone Morphogenic Protein Antagonist Noggin (2006)

It is currently not known whether dopamine (DA) neurons derived from human embryonic stem cells (hESCs) can survive in vivo and alleviate symptoms in models of Parkinson disease (PD). Here, we report the use of Noggin (a bone morphogenic protein antagonist) to induce neuroectodermal cell development and increase the yield of DA neurons from hESCs. A combination of stromal-derived inducing activity and Noggin markedly enhanced the generation of neuroepithelial progenitors that could give rise to DA neurons. In addition, Noggin diminished the occurrence of a fibroblast-like Nestin-positive precursor population that differentiated into myocytes. After transplantation of differentiated hESCs to a rodent model of PD, some grafts contained human midbrain-like DA neurons. This protocol demonstrates hESC derivation and survival of human DA neurons appropriate for cell therapy in PD.
Algorithms and Trade-Offs in Multicast Service Overlay Design (2006)

The Multicast Service Overlay Network (MSON) has been recently introduced to address some of the deployment and maintenance problems of IP multicast and application-level multicast. An MSON is essentially a backbone service overlay provisioned by an MSON provider and designed to “multiplex” multiple-user overlays. It consists of service nodes or proxies deployed by the provider. The proxies are strategically deployed to form a backbone overlay and provide multicasting functionalities for supporting many user groups simultaneously. The MSON provider designs the backbone overlay for a large user population and can therefore enjoy large-scale economies and benefits. Since the deployment of an MSON is a capital-intensive investment, it is very imperative to carefully design the MSON so that the provider can make the best revenue out of this investment. In this article, the authors formulate the MSON design problem by taking into account operational costs of the MSON provider. They then explore three subproblems: overlay proxy placement, overlay link selection, and bandwidth dimensioning. For each of these subproblems, the authors present several algorithms and discuss their design trade-offs. By simulations, they investigate the effectiveness of different overlay design algorithms, analyze their impact on multicast performance, and suggest some practical solutions for MSON design.
Expression of human full-length MUC1 inhibits the proliferation and migration of a B16 mouse melanoma cell line (2013)

Mucin 1 (MUC1) is a large transmembrane glycoprotein that is aberrantly overexpressed in most adenocarcinomas and certain hematological malignancies. MUC1 is known to function as an oncogene with roles in both tumor formation and progression, making it a potential target for immunotherapy. B16-MUC1 cells with human full-length MUC1 are frequently used to study the antitumor activities of MUC1-based vaccines. However, we found that the growth of B16-MUC1 cells was significantly reduced in vitro. Therefore, in this study, we established two MUC1-positive clones, B16-MUC1 9-12 and B16-MUC1 9-23, and one empty vector control clone, B16-neo, to investigate the effects of MUC1 on the cancer-related characteristics of B16 cells in vitro and in vivo. Our results demonstrated that, compared with MUC1-negative cells, cells expressing MUC1 exhibited decreased cell proliferation, increased cell cycle arrest and reduced cell migratory and invasive capacities. We further investigated several MUC1-related molecules of the β-catenin pathway, and found that the expression of MUC1 decreased the translocation of β-catenin into the nucleus, reduced the activity of T cell factor (TCF) and blocked the expression of cyclin D1 and c-Myc. Moreover, when inoculated into BALB/c nude mice, cells expressing MUC1 developed smaller tumors compared with the control cells. These results demonstrate that MUC1 expression negatively affects the malignancy of B16 cells, and suggest that the regulatory mechanisms of MUC1 as an oncoprotein are more complex than previously appreciated.
Determination of Surface-active Agents. VIII. Infrared Determination of the Proportion of Ethylene Oxide and Propylene Oxide in Pluronic (1967)

A new determination method of the proportion of ethylene oxide and propylene oxide in Pluronic was devised, the stretching bands of methyl and methylene group being used as the key bands. The proportion was determined within an error of ±5% without regard to the difference of molecular weight of propylene oxide condensate.
Molecular Cloning and Nucleotide Sequence of DNA Complementary to Rat Ribosomal Protein S26 Messenger RNA1 (1985)

A cDNA clone specific for rat ribosomal protein S26 was isolated by a positive hybridization translation assay from a cDNA library made for 8-9S poly(A)mRNA from regenerating rat liver. The nucleotide sequence of the cDNA was determined. The sequence contains 23 base pairs in the 5' noncoding region, 345 base pairs in the protein coding region and 67 base pairs in the 3' noncoding region besides the poly(A) tail. The primary structure of the protein S26 was deduced from the nucleotide sequence. It consists of 115 amino acids. Its molecular weight is 13,015 and its pI is about 11.1. The calculated amino acid composition is consistent with the reported composition of S26. From the results of Southern blot analysis, the protein S26 appears to have multiple genes.
21 W broad area near-diffraction-limited semiconductor amplifier (1992)

A 600 μm wide broad area single pass GaAlAs traveling wave amplifier emitted 21 W in pulsed operation. The far-field was dominated by a near-diffraction limited 0.08° wide lobe, with 16 W measured in a 0.9° angular aperture. Current dependent scattering of the output beam power to outside of the diffraction-limited lobe was observed.
Nodular basal cell carcinoma is associated with increased hyaluronan homeostasis (2010)

These results indicate that HA homeostasis in nodular BCC shows distinct features which may be helpful in understanding the complex behaviour of nodular subtype of BCC, thus eventually leading to new treatment strategies.
Herpes simplex virus type 1 glycoprotein E is not indispensable for viral infectivity (1987)

A mutant of the herpes simplex virus type 1 Angelotti was isolated in which 87% of the coding region of glycoprotein E (gE) was deleted and replaced by a functional neomycin resistance gene of the Tn5 transposon. The mutant was characterized by restriction enzyme analyses and Southern blotting. Western blotting of proteins and immunofluorescence assays revealed that gE was completely absent and that the Fc receptor was not expressed in cells infected with the mutant. The fact that this mutant was viable and that it replicated to a slightly lower titer than did the wild-type virus suggests that the presence of gE is not a prerequisite of viral infectivity in tissue culture.
Antimicrobial Metabolites from a Bacterial Symbiont (1995)

Two types of antibiotics, namely, indoles and dithiolopyrrolones, have been isolated and identified from Xenorhabdus bovienii A2. Compounds 1 and 2 showed strong activity against Cryptococcus neoformans, compounds 3 and 4 showed strong activity against Botrytis cinerea, and compounds 1, 3, and 4 showed significant activity against Phytophthora infestants (2 was not tested). In addition, two lower homologues of xenorhabdins 5 and 6, namely, 6-(N-3'-methylbutanamido)-4,5-dihydro-1,2-dithiolo[4,3-b]pyr rol-5- one [7] and 6-(N-butanamido)[4,5-dihydro-1,2-dithiolo[4,3-b]pyrrol-5-one [8], have been isolated and characterized for the first time.
Fate of immunoprecipitable protein kinase C in GH3 cells treated with phorbol 12-myristate 13-acetate. (1985)

The effect of phorbol 12-myristate 13-acetate (PMA) on protein kinase C was studied by metabolically labeling GH3 cells with [35S]methionine and using a polyclonal antibody raised against rat brain protein kinase C to immunoprecipitate the enzyme. PMA accelerates the loss of immunologically reactive protein kinase C from the cells in a time- and dose-dependent manner. The half-life of the enzyme in cells treated with 400 nM PMA was 2 h whereas in control cells 60-70% of the enzyme was still detectable after 24 h. The concentration of PMA required to reduce cellular protein kinase C 50% after 24 h was 130 nM. PMA also induced the translocation of [35S]Met-labeled protein kinase C from the cytosol to the membranes in a concentration-dependent manner. Less protein kinase C was translocated to membranes when cells were treated with 20 nM PMA than when they were exposed to 400 nM PMA. In the latter case, most of the labeled protein kinase C became membrane-associated. Maximal translocation was evident after 15 min of incubation with either concentration of PMA and was followed by degradation of the membrane-associated enzyme. The rate of degradation of membrane-associated protein kinase C was the same with both concentrations of PMA. In cells treated with 20 nM PMA, disappearance of [35S]Met-labeled protein kinase C from the cytosolic fraction occurred in two phases, a rapid decrease characteristic of the membrane-associated enzyme, followed by a slower loss similar to that seen in control cells. The results indicate that turnover of protein kinase C is enhanced by membrane association.
Isolation and Characterization of a cDNA That Encodes Maize Glutamate Dehydrogenase (1995)

A full-length cDNA clone, pMGDH1, encoding maize NADH-glutamate dehydrogenase (NADH-GDH) was isolated from a maize root cDNA library. The identity of the cDNA was established by the coincidence of the structure of the purified protein with that inferred from the nucleotide sequence of the cDNA. pMGDH1 had a cDNA insert of 1,638 bp and the open reading frame encoded 411 amino acid residues. The deduced amino acid sequence was similar to putative partial sequences of GDHs from higher plants and to the sequences of GDHs from organisms as diverse as mammals and bacteria. The NH2-terminal sequence deduced from the open reading frame had a typical structure that is associated with the import of proteins into the mitochondrial matrix. The cDNA hybridized to an RNA of about 1.6 kb. This transcript was more abundant in roots than in leaves and was localized in the bundle sheath cells in leaf tissues. Analysis of genomic DNA by Southern hybridization suggested the existence of gene(s) for another NADH-GDH subunit(s).
XIII. Yeast sequencing reports. SED6 is identical to ERG6, and encodes a putative methyltransferase required for ergosterol synthesis (1994)

Luminal endoplasmic reticulum (ER) proteins carry a sorting signal that allows them to be retrieved from the Golgi apparatus by a specific receptor. In yeast, this receptor is encoded by the ERD2 gene. Although retrieval of ER proteins does not appear to be an essential process, cells lacking ERD2 do not grow. Several multicopy suppressors of this growth defect have been isolated. The sequence of one of these, SED6, is presented here. Its product contains motifs characteristic of methyltransferases, and it is identical to ERG6, the presumed structural gene for S-adenosylmethionine:delta 24-sterol-C-methyltransferase. The gene is located adjacent to PDR4, near the centromere of chromosome XIII.
Exploiting Shallow Linguistic Information for Relation Extraction from Biomedical Literature (2006)

We propose an approach for extracting relations between entities from biomedical literature based solely on shallow linguistic information. We use a combination of kernel functions to integrate two different information sources: (i) the whole sentence where the relation appears, and (ii) the local contexts around the interacting entities. We performed experiments on extracting gene and protein interactions from two different data sets. The results show that our approach outperforms most of the previous methods based on syntactic and semantic information. 1
Identification of benzodiazepine Ro5-3335 as an inhibitor of CBF leukemia through quantitative high throughput screen against RUNX1–CBFβ interaction (2012)

Core binding factor (CBF) leukemias, those with translocations or inversions that affect transcription factor genes RUNX1 or CBFB, account for ~24% of adult acute myeloid leukemia (AML) and 25% of pediatric acute lymphocytic leukemia (ALL). Current treatments for CBF leukemias are associated with significant morbidity and mortality, with a 5-y survival rate of ~50%. We hypothesize that the interaction between RUNX1 and CBFβ is critical for CBF leukemia and can be targeted for drug development. We developed high-throughput AlphaScreen and time-resolved fluorescence resonance energy transfer (TR-FRET) methods to quantify the RUNX1-CBFβ interaction and screen a library collection of 243,398 compounds. Ro5-3335, a benzodiazepine identified from the screen, was able to interact with RUNX1 and CBFβ directly, repress RUNX1/CBFB-dependent transactivation in reporter assays, and repress runx1-dependent hematopoiesis in zebrafish embryos. Ro5-3335 preferentially killed human CBF leukemia cell lines, rescued preleukemic phenotype in a RUNX1-ETO transgenic zebrafish, and reduced leukemia burden in a mouse CBFB-MYH11 leukemia model. Our data thus confirmed that RUNX1-CBFβ interaction can be targeted for leukemia treatment and we have identified a promising lead compound for this purpose.
Delineation of Diverse Macrophage Activation Programs in Response to Intracellular Parasites and Cytokines (2010)

This study provides global gene expression data for a diverse set of biologically significant pathogens and cytokines and identifies the relationships between macrophage activation states induced by these stimuli. By comparing macrophage activation programs to pathogens and cytokines under identical experimental conditions, we provide new insights into how macrophage responses to kinetoplastids correlate with the overall range of macrophage activation states.
Peritoneal carcinomatosis (2013)

Several gastrointestinal and gynecological malignancies have the potential to disseminate and grow in the peritoneal cavity. The occurrence of peritoneal carcinomatosis (PC) has been shown to significantly decrease overall survival in patients with liver and/or extraperitoneal metastases from gastrointestinal cancer. During the last three decades, the understanding of the biology and pathways of dissemination of tumors with intraperitoneal spread, and the understanding of the protective function of the peritoneal barrier against tumoral seeding, has prompted the concept that PC is a loco-regional disease: in absence of other systemic metastases, multimodal approaches combining aggressive cytoreductive surgery, intraperitoneal hyperthermic chemotherapy and systemic chemotherapy have been proposed and are actually considered promising methods to improve loco-regional control of the disease, and ultimately to increase survival. The aim of this review article is to present the evidence on treatment of PC in different tumors, in order to provide patients with a proper surgical and multidisciplinary treatment focused on optimal control of their locoregional disease.
Identification of Burkholderia cenocepacia Genes Required for Bacterial Survival In Vivo (2004)

Burkholderia cenocepacia (formerly Burkholderia cepacia complex genomovar III) causes chronic lung infections in patients with cystic fibrosis. In this work, we used a modified signature-tagged mutagenesis (STM) strategy for the isolation of B. cenocepacia mutants that cannot survive in vivo. Thirty-seven specialized plasposons, each carrying a unique oligonucleotide tag signature, were constructed and used to examine the survival of 2,627 B. cenocepacia transposon mutants, arranged in pools of 37 unique mutants, after a 10-day lung infection in rats by using the agar bead model. The recovered mutants were screened by real-time PCR, resulting in the identification of 260 mutants which presumably did not survive within the lungs. These mutants were repooled into smaller pools, and the infections were repeated. After a second screen, we isolated 102 mutants unable to survive in the rat model. The location of the transposon in each of these mutants was mapped within the B. cenocepacia chromosomes. We identified mutations in genes involved in cellular metabolism, global regulation, DNA replication and repair, and those encoding bacterial surface structures, including transmembrane proteins and cell surface polysaccharides. Also, we found 18 genes of unknown function, which are conserved in other bacteria. A subset of 12 representative mutants that were individually examined using the rat model in competition with the wild-type strain displayed reduced survival, confirming the predictive value of our STM screen. This study provides a blueprint to investigate at the molecular level the basis for survival and persistence of B. cenocepacia within the airways.
Haemodynamic influences on kidney oxygenation: Clinical implications of integrative physiology (2012)

Renal blood flow, local tissue perfusion and blood oxygen content are the major determinants of oxygen delivery to kidney tissue. Arterial pressure and segmental vascular resistance influence kidney oxygen consumption through effects on glomerular filtration rate and sodium reabsorption. Diffusive shunting of oxygen from arteries to veins in the cortex and from descending to ascending vasa recta in the medulla limits oxygen delivery to renal tissue. Oxygen shunting depends on the vascular network, renal haemodynamics and kidney oxygen consumption. Consequently, the impact of changes in renal haemodynamics on tissue oxygenation cannot necessarily be predicted intuitively and, instead, requires the integrative approach offered by computational modelling and multiple measuring modalities. Tissue hypoxia is a hallmark of acute kidney injury (AKI) arising from multiple initiating insults, including ischaemia-reperfusion injury, radiocontrast administration, cardiopulmonary bypass surgery, shock and sepsis. Its pathophysiology is defined by inflammation and/or ischaemia resulting in alterations in renal tissue oxygenation, nitric oxide bioavailability and oxygen radical homeostasis. This sequence of events appears to cause renal microcirculatory dysfunction, which may then be exacerbated by the inappropriate use of therapies common in peri-operative medicine, such as fluid resuscitation. The development of new ways to prevent and treat AKI requires an integrative approach that considers not just the molecular mechanisms underlying failure of filtration and tissue damage, but also the contribution of haemodynamic factors that determine kidney oxygenation. The development of bedside monitors allowing continuous surveillance of renal haemodynamics, oxygenation and function should facilitate better prevention, detection and treatment of AKI.
Presynaptic association of Rad51 protein with selected sites in meiotic chromatin. (1996)

Eukaryotic homologs of Escherichia coli Rec-A protein have been shown to form nucleoprotein filaments with single-stranded DNA that recognize homologous sequences in duplex DNA. Several recent reports in four widely diverse species have demonstrated the association of RecA homologs with meiotic prophase chromatin. The current immunocytological study on mouse spermatocytes and oocytes shows that a eukaryotic homolog, Rad5l, associates with a subset of chromatin sites as early as premeiotic S phase, hours before either the appearance of precursors of synaptonemal complexes or the initiation of synapsis. When homologous chromosomes do begin to pair, the Rad5l-associated sequences are sites of initial contact between homologues and of localized DNA synthesis. Distribution of Rad5l foci on the chromatin of fully synapsed bivalents at early pachynema corresponds to an R-band pattern of mitotic chromosomes. R-bands are known to be preferred sites of both synaptic initiation and recombination. The time course of appearance of Rad51 association with chromatin, its distribution, and its interaction with other Rad5l-associated sequences suggests that it plays an important role preselection of sequences and synaptic initiation.
An anti-CD45RO/RB monoclonal antibody modulates T cell responses via induction of apoptosis and generation of regulatory T cells (2005)

The effects of a chimeric monoclonal antibody (chA6 mAb) that recognizes both the RO and RB isoforms of the transmembrane protein tyrosine phosphatase CD45 on human T cells were investigated. Chimeric A6 (chA6) mAb potently inhibited antigen-specific and polyclonal T cell responses. ChA6 mAb induced activation-independent apoptosis in CD4(+)CD45RO/RB(high) T cells but not in CD8(+) T cells. In addition, CD4(+) T cell lines specific for tetanus toxoid (TT) generated in the presence of chA6 mAb were anergic and suppressed the proliferation and interferon (IFN)-gamma production by TT-specific effector T cells by an interleukin-10-dependent mechanism, indicating that these cells were equivalent to type 1 regulatory T cells. Similarly, CD8(+) T cell lines specific for the influenza A matrix protein-derived peptide (MP.58-66) generated in the presence of chA6 mAb were anergic and suppressed IFN-gamma production by MP.58-66-specific effector CD8(+) T cells. Furthermore, chA6 mAb significantly prolonged human pancreatic islet allograft survival in nonobese diabetic/severe combined immunodeficiency mice injected with human peripheral blood lymphocytes (hu-PBL-NOD/SCID). Together, these results demonstrate that the chA6 mAb is a new immunomodulatory agent with multiple modes of action, including deletion of preexisting memory and recently activated T cells and induction of anergic CD4(+) and CD8(+) regulatory T cells.
Wide‐Range Tuning and Enhancement of Organic Long‐Persistent Luminescence Using Emitter Dopants (2018)

Most long-persistent luminescent (LPL) materials, which slowly release energy absorbed from ambient light, are based on inorganic compounds. Organic long-persistent luminescent (OLPL) systems have advantages over inorganic LPL materials in terms of solubility, transparency, and flexibility. Here, the characteristics of OLPL emission are improved by doping emitter molecules into an OLPL matrix. Greenish-blue to red and even warm white emission are achieved by energy transfer from exciplex in the OLPL matrix to the emitter dopants. The dopants also improve brightness and emission duration through efficient radiative decay and the trapping of electrons, respectively. This technique will enable the development of a wide range of organic glow-in-the-dark paints.
Once‐Daily, Controlled‐Release Tramadol and Sustained‐Release Diclofenac Relieve Chronic Pain due to Osteoarthritis: A Randomized Controlled Trial (2008)

CR tramadol is as effective as SR diclofenac in the treatment of pain due to knee or hip osteoarthritis, with the potential for fewer of the serious side effects that characterize nonsteroidal anti-inflammatory drug administration.
Design of an efficient ambient WiFi energy harvesting system (2012)

This study is focused on equipping wireless devices (including sensors) with novel, high-efficiency circuitry to harvest and convert ambient radio frequency (RF) power to direct current (dc). Key components of this technology are (a) miniaturised antenna and (b) high-efficiency rectifying circuit. The first is responsible for capturing the RF waves, and the latter converts the RF energy to dc. A major challenge is the design of novel circuitry to generate a battery-like voltage from very low incoming RF energy. Under this study, the authors designed a novel RF power harvesting front-end whose conversion efficiency is significantly improved at low RF power levels (&lt;−20 dBm) as compared to existing technologies. Thus, the new circuitry can harvest ambient and widely available RF energy, making a game changing technology for powering mobile devices. In this study, the authors demonstrate this technology by using it to power a commercially available temperature and humidity meter with an LCD display. The latter is powered using nothing more than ambient WiFi signals in an office environment.