gebhart/patrepeval huggingface dataset:
Tumor microenvironment and progression (2011)

Tumor blood vessels are heterogeneous, of at least six distinct types, are induced primarily by vascular endothelial growth factor-A (VEGF-A), and provide a potentially useful therapeutic target. Breast cancer is characterized by changes in the microenvironment that result in altered tensional homeostasis. Also, breast cancers arise as the result of epigenetic as well as genetic changes. Tumor blood vessel pericytes result, in part, from bone marrow precursor cells, and VEGF is a negative regulator of glioblastoma tumor cell invasion.
Substrate Recognition and Ubiquitination of SCFSkp2/Cks1 Ubiquitin-Protein Isopeptide Ligase (2007)

p27, an important cell cycle regulator, blocks the G(1)/S transition in cells by binding and inhibiting Cdk2/cyclin A and Cdk2/cyclin E complexes (Cdk2/E). Ubiquitination and subsequent degradation play a critical role in regulating the levels of p27 during cell cycle progression. Here we provide evidence suggesting that both Cdk2/E and phosphorylation of Thr(187) on p27 are essential for the recognition of p27 by the SCF(Skp2/Cks1) complex, the ubiquitin-protein isopeptide ligase (E3). Cdk2/E provides a high affinity binding site, whereas the phosphorylated Thr(187) provides a low affinity binding site for the Skp2/Cks1 complex. Furthermore, binding of phosphorylated p27/Cdk2/E to the E3 complex showed positive cooperativity. Consistently, p27 is also ubiquitinated in a similarly cooperative manner. In the absence of p27, Cdk2/E and Cks1 increase Skp2 phosphorylation. This phosphorylation enhances Skp2 auto-ubiquitination, whereas p27 inhibits both phosphorylation and auto-ubiquitination of Skp2.
Synthesis and in vitro evaluation of 18F‐β‐carboline alkaloids as PET ligands (2008)

Abstract A one‐step 18 F‐labelling strategy was used to prepare four 18 F‐labelled analogues of 7‐methoxy‐1‐methyl‐ 9H ‐β‐carboline (harmine): 7‐(2‐[ 18 F]fluoroethoxy)‐1‐methyl‐9 H ‐β‐carboline (5), 7‐(3‐[ 18 F]fluoro‐propoxy)‐1‐methyl‐9 H ‐β‐carboline (6), 7‐[2‐(2‐[ 18 F]fluoroethoxy)ethoxy]‐1‐methyl‐9 H ‐β‐carboline (7), and 7‐{2‐[2‐(2‐[ 18 F]fluoroethoxy)ethoxy]‐ethoxy}‐1‐methyl‐9 H ‐β‐carboline (8). These were synthesized as potential positron emission tomography ligands for monoamine oxidase A (MAO‐A). A solution of pure labelled compound in buffer was obtained in &lt;70 min from end of radionuclide production, with a decay‐corrected yield of up to 23%. The average specific binding to MAO‐A in rat brain, determined by autoradiography experiments, was highest for compounds 7 and 8 (89±2 and 96±1%, respectively), which was obtained at &lt;1 nM radioligand concentration. Copyright © 2008 John Wiley &amp; Sons, Ltd.
Dihydroartemisinin induces apoptosis and sensitizes human ovarian cancer cells to carboplatin therapy (2008)

Abstract The present study was designed to determine the effects of artemisinin (ARS) and its derivatives on human ovarian cancer cells, to evaluate their potential as novel chemotherapeutic agents used alone or in combination with a conventional cancer chemotherapeutic agent, and to investigate their underlying mechanisms of action. Human ovarian cancer cells (A2780 and OVCAR‐3), and immortalized non‐tumourigenic human ovarian surface epithelial cells (IOSE144), were exposed to four ARS compounds for cytotoxicity testing. The in vitro and in vivo antitumour effects and possible underlying mechanisms of action of dihydroartemisinin (DHA), the most effective compound, were further determined in ovarian cancer cells. ARS compounds exerted potent cytotoxicity to human ovarian carcinoma cells, with minimal effects on non‐tumourigenic ovarian surface epithelial (OSE) cells. DHA inhibited ovarian cancer cell growth when administered alone or in combination with carboplatin, presumably through the death receptor‐ and, mitochondrion‐mediated caspase‐dependent apoptotic pathway. These effects were also observed in in vivo ovarian A2780 and OVCAR‐3 xenograft tumour models. In conclusion, ARS derivatives, particularly DHA, exhibit significant anticancer activity against ovarian cancer cells in vitro and in vivo , with minimal toxicity to non‐tumourigenic human OSE cells, indicating that they may be promising therapeutic agents for ovarian cancer, either used alone or in combination with conventional chemotherapy.
Regulation of granulocyte colony-stimulating factor and granulocyte- macrophage colony-stimulating factor expression by oncostatin M (1993)

Oncostatin M (OM) is structurally and functionally related to a subclass of hematopoietic cytokines including leukemia-inhibitory factor (LIF), ciliary neurotrophic factor (CNTF), granulocyte colony-stimulating factor (G-CSF), and interleukin-6 (IL-6). Using human endothelial cells (HEC) as a model for cytokine regulation of hematopoietic growth factor expression, we tested OM as an inducer of colony-stimulating activity. Colony-forming cell assays supplemented with culture supernatants from OM-treated HEC contained a threefold increase in colony-forming unit granulocyte-macrophage colonies. Specific immunoassay (enzyme-linked immunosorbent assay) of culture supernatants indicated that OM treatment of HEC resulted in a dose- and time-dependent increase in the accumulation of G-CSF and granulocyte-macrophage CSF (GM-CSF) (> 28-fold). The ED50 for OM induction of G-CSF and GM-CSF protein expression was 17 and 7 pmol/L, respectively. Increased protein expression was associated with a similar increase in steady-state expression of G-CSF and GM-CSF mRNA. Furthermore, a period of 12 to 24 hours elapsed before there were measurable increases in CSF expression, suggesting that OM may stimulate CSF production through a mechanism requiring the synthesis or activation of a secondary mediating factor or pathway. These findings provide the first evidence that OM may regulate myelopoiesis by inducing the cellular expression of hematopoietic growth factors.
Enhanced Production of Functional Proteins from Defective Genes (2004)

Nonsense mutations are associated with a host of genetic disorders. The protein products encoded by genes containing these mutations are either truncated or completely missing. Recently, members of the aminoglycoside family of antibiotics have been found to induce the ribosome to read past these inappropriately inserted stop codons, albeit at extremely modest efficiencies. We report herein a strategy that enhances the production of functional proteins from the corresponding mutated genes.
Forensically Relevant SNP Classes (2008)

Forensic samples that contain too little template DNA or are too degraded require alternate genetic marker analyses or approaches to what is currently used for routine casework. Single nucleotide polymorphisms (SNPs) offer promise to support forensic DNA analyses because of an abundance of potential markers, amenability to automation, and potential reduction in required fragment length to only 60-80 bp. The SNP markers will serve an important role in analyzing challenging forensic samples, such as those that are very degraded, for augmenting the power of kinship analyses and family reconstructions for missing persons and unidentified human remains, as well as for providing investigative lead value in some cases without a suspect (and no genetic profile match in CODIS). The SNPs for forensic analyses can be divided into four categories: identity-testing SNPs; lineage informative SNPs; ancestry informative SNPs; and phenotype informative SNPs. In addition to discussing the applications of these different types of SNPs, this article provides some discussion on privacy issues so that society and policymakers can be more informed.
Proneural bHLH neurogenin 2 differentially regulates Nurr1‐induced dopamine neuron differentiation in rat and mouse neural precursor cells in vitro (2008)

Roles of Nurr1 and neurogenin 2 (Ngn2) have been shown in midbrain dopamine (DA) neuron development. We present here rat and mouse species-dependent differences of Nurr1 and Ngn2 actions in DA neuron differentiation. Nurr1 exogene expression caused an efficient generation of tyrosine hydroxylase (TH)-positive DA cells from rat neural precursor cells (NPCs). Nurr1-induced TH+ cell yields were low and highly variable depending on the origins of NPCs in mouse cultures. Coexpression of Ngn2 repressed Nurr1-induced generation of TH+ cells in rat cultures. In clear contrast, a robust enhancement in Nurr1-induced DA cell yields was observed in mouse NPCs by Ngn2. These findings imply that DA neurons may develop differently in the midbrains of these two species.
Space-Time Behavior-Based Correlation-OR-How to Tell If Two Underlying Motion Fields Are Similar Without Computing Them? (2007)

We introduce a behavior-based similarity measure which tells us whether two different space-time intensity patterns of two different video segments could have resulted from a similar underlying motion field. This is done directly from the intensity information, without explicitly computing the underlying motions. Such a measure allows us to detect similarity between video segments of differently dressed people performing the same type of activity. It requires no foreground/background segmentation, no prior learning of activities, and no motion estimation or tracking. Using this behavior-based similarity measure, we extend the notion of 2-dimensional image correlation into the 3-dimensional space-time volume, thus allowing to correlate dynamic behaviors and actions. Small space-time video segments (small video clips) are "correlated" against entire video sequences in all three dimensions (x,y, and t). Peak correlation values correspond to video locations with similar dynamic behaviors. Our approach can detect very complex behaviors in video sequences (e.g., ballet movements, pool dives, running water), even when multiple complex activities occur simultaneously within the field-of-view of the camera. We further show its robustness to small changes in scale and orientation of the correlated behavior.
IgE stimulates human and mouse arterial cell apoptosis and cytokine expression and promotes atherogenesis in Apoe–/– mice (2011)

IgE has a key role in the pathogenesis of allergic responses through its ability to activate mast cells via the receptor FcεR1. In addition to mast cells, many cell types implicated in atherogenesis express FcεR1, but whether IgE has a role in this disease has not been determined. Here, we demonstrate that serum IgE levels are elevated in patients with myocardial infarction or unstable angina pectoris. We found that IgE and the FcεR1 subunit FcεR1α were present in human atherosclerotic lesions and that they localized particularly to macrophage-rich areas. In mice, absence of FcεR1α reduced inflammation and apoptosis in atherosclerotic plaques and reduced the burden of disease. In cultured macrophages, the presence of TLR4 was required for FcεR1 activity. IgE stimulated the interaction between FcεR1 and TLR4, thereby inducing macrophage signal transduction, inflammatory molecule expression, and apoptosis. These IgE activities were reduced in the absence of FcεR1 or TLR4. Furthermore, IgE activated macrophages by enhancing Na+/H+ exchanger 1 (NHE1) activity. Inactivation of NHE1 blocked IgE-induced macrophage production of inflammatory molecules and apoptosis. Cultured human aortic SMCs (HuSMCs) and ECs also exhibited IgE-induced signal transduction, cytokine expression, and apoptosis. In human atherosclerotic lesions, SMCs and ECs colocalized with IgE and TUNEL staining. This study reveals what we believe to be several previously unrecognized IgE activities that affect arterial cell biology and likely other IgE-associated pathologies in human diseases.
Extensible Messaging and Presence Protocol (XMPP): Core (2004)

The Extensible Messaging and Presence Protocol (XMPP) is an
application profile of the Extensible Markup Language (XML) that
enables the near-real-time exchange of structured yet extensible data
between any two or more network entities. This document defines
XMPP's core protocol methods: setup and teardown of XML streams,
channel encryption, authentication, error handling, and communication
primitives for messaging, network availability (presence), and
request-response interactions. This document obsoletes RFC 3920.
[STANDARDS-TRACK]
Projecting Cancer Incidence and Deaths to 2030: The Unexpected Burden of Thyroid, Liver, and Pancreas Cancers in the United States (2014)

Cancer incidence and deaths in the United States were projected for the most common cancer types for the years 2020 and 2030 based on changing demographics and the average annual percentage changes in incidence and death rates. Breast, prostate, and lung cancers will remain the top cancer diagnoses throughout this time, but thyroid cancer will replace colorectal cancer as the fourth leading cancer diagnosis by 2030, and melanoma and uterine cancer will become the fifth and sixth most common cancers, respectively. Lung cancer is projected to remain the top cancer killer throughout this time period. However, pancreas and liver cancers are projected to surpass breast, prostate, and colorectal cancers to become the second and third leading causes of cancer-related death by 2030, respectively. Advances in screening, prevention, and treatment can change cancer incidence and/or death rates, but it will require a concerted effort by the research and healthcare communities now to effect a substantial change for the future.
Two New Steroidal Alkaloids, 20-Isoveratramine and Verapatuline, from the Roots and Rhizomes of Veratrum patulum (1998)

Roots and rhizomes of Veratrum patulum L. (Liliaceae), used as a source of the Chinese crude drug "Li-lu", have yielded two new steroidal alkaloids, 20-isoveratramine (1) and verapatuline (2), along with three known alkaloids, veratramine (3), veratrosine (4), and jervine (5). Structures of new alkaloids 1 and 2 were determined to be a C-20 epimer of 3 and N-(methoxycarbonyl)jervine, respectively, by the use of spectral data including 2D NMR.
Synthesis of Well-Defined Block Copolymers Tethered to Polysilsesquioxane Nanoparticles and Their Nanoscale Morphology on Surfaces (2001)

ADVERTISEMENT RETURN TO ISSUEPREVCommunicationNEXTSynthesis of Well-Defined Block Copolymers Tethered to Polysilsesquioxane Nanoparticles and Their Nanoscale Morphology on SurfacesJeffrey Pyun, Krzysztof Matyjaszewski, Tomasz Kowalewski, Daniel Savin, Gary Patterson, Guido Kickelbick, and Nicola HuesingView Author Information Department of Chemistry, Carnegie Mellon University 4400 Fifth Avenue, Pittsburgh, Pennsylvania 15213 Technische Universität Wien Getreidemarkt 9/153, A-1060 Wien Cite this: J. Am. Chem. Soc. 2001, 123, 38, 9445–9446Publication Date (Web):August 30, 2001Publication History Received29 January 2001Published online30 August 2001Published inissue 1 September 2001https://pubs.acs.org/doi/10.1021/ja010241mhttps://doi.org/10.1021/ja010241mrapid-communicationACS PublicationsCopyright © 2001 American Chemical SocietyRequest reuse permissionsArticle Views1934Altmetric-Citations160LEARN 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-AlertscloseSupporting Info (1)»Supporting Information Supporting Information SUBJECTS:Colloidal particles,Nanocomposites,Nanoparticles,Radical polymerization,Transmission electron microscopy Get e-Alerts
Genetic Changes In The Pathogenesis Of Lung Cancer (1989)

CD40 is a cell-surface member of the TNF (tumor necrosis factor) receptor superfamily. Upon activation, CD40 can license dendritic cells to promote antitumor T cell activation and re-educate macrophages to destroy tumor stroma. Numerous agonist CD40 ...Read More
Immunization of Chickens with Newcastle Disease Virus Expressing H5 Hemagglutinin Protects against Highly Pathogenic H5N1 Avian Influenza Viruses (2009)

Our results suggest that these chimeric viruses have potential as safe and effective bivalent vaccines against NDV and. HPAIV. These vaccines will be convenient and affordable, which will be highly beneficial to the poultry industry. Furthermore, immunization with these vaccines will permit serological differentiation of vaccinated and avian influenza field virus infected animals.
A noisy-channel approach to question answering (2003)

We introduce a probabilistic noisy-channel model for question answering and we show how it can be exploited in the context of an end-to-end QA system. Our noisy-channel system outperforms a state-of-the-art rule-based QA system that uses similar resources. We also show that the model we propose is flexible enough to accommodate within one mathematical framework many QA-specific resources and techniques, which range from the exploitation of WordNet, structured, and semi-structured databases to reasoning, and paraphrasing.
Implementation of the Meteorology and Oceanography Geospatial Initiative at the Naval Oceanographic Office (2002)

The Naval Oceanographic Office (NAVOCEANO) is charged with the collection and processing of oceanographic data worldwide in direct support of military operations. They are also a co-producer of digital products with the National Imagery and Mapping Agency (NIMA). They currently provide more than 1600 products a year in support of warfighter operations. The Meteorology and Oceanography (METOC) Geospatial Initiative (MGI) is designed to be part of an overall end-to-end reengineering of their production so that features can be derived directly from our data holdings, properly attributed, and made available to both NIMA and Department of Defense (DOD) for military operations. They provide products, to numerous multi-agency customers including Navy, Marine Corps, Army, Air Force, U.S. Coast Guard, Department of Defense Commanders in Chief, and U.S. Government agencies. MGI will reengineer NAVOCEANO production processes to build METOC datasets as fully attributed geospatial information. The datasets will comply with DOD-adopted feature and attribute coding standards. In this way, their products will be interoperable with those of NIMA. They anticipate that these products will be directly usable in military operations, especially on geographic information system (GIS) enabled electronic displays. The purpose of this effort is to provide systems engineering services, in phased increments, to bring NAVOCEANO production areas within the domain of standards-driven co-production. This paper describes the background and rationale for entering into a major reengineering effort that will result in a geospatially enabled production environment at NAVOCEANO.
An Effective Method for Alcohol Preparation by Hydrolysis of Organohalides in the Presence of Copper and its Salts in Aqueous DMSO (1995)

Hydrolysis of alkyl halides in the presence of copper and its salts in aqueous DMSO (molar ratio organohalide:CuSO4·5H2O:DMSO:H2O 1:1:10–20:12–25) at 100–117 °C gives alcohols in high yields. Aryl halides containing no activating substituents are inert under the reaction conditions.
Food and Oral Antineoplastics: More Than Meets the Eye (2010)

Food can alter the bioavailability of orally administered drugs. Description of food effects in product labels and information about administration in relation to food are influenced by a variety of factors. Because food effects can change drug efficacy and toxicity, it is important that physicians and patients be aware of them.
Gold Nanorod-sensitized Cell Death: Microscopic Observation of Single Living Cells Irradiated by Pulsed Near-infrared Laser Light in the Presence of Gold Nanorods (2006)

Abstract Pulsed near-infrared (near-IR) laser irradiation damaged cultured cells in the presence of phosphatidylcholine-passivated gold nanorods (PC-NRs). When single cells were irradiated with a focused pulsed near-IR laser, photoreaction of the PC-NRs caused damage within a very small area around the PC-NRs, and achieved selective cell death of single cells.
Massively parallel whole genome amplification for single-cell sequencing using droplet microfluidics (2017)

Massively parallel single-cell genome sequencing is required to further understand genetic diversities in complex biological systems. Whole genome amplification (WGA) is the first step for single-cell sequencing, but its throughput and accuracy are insufficient in conventional reaction platforms. Here, we introduce single droplet multiple displacement amplification (sd-MDA), a method that enables massively parallel amplification of single cell genomes while maintaining sequence accuracy and specificity. Tens of thousands of single cells are compartmentalized in millions of picoliter droplets and then subjected to lysis and WGA by passive droplet fusion in microfluidic channels. Because single cells are isolated in compartments, their genomes are amplified to saturation without contamination. This enables the high-throughput acquisition of contamination-free and cell specific sequence reads from single cells (21,000 single-cells/h), resulting in enhancement of the sequence data quality compared to conventional methods. This method allowed WGA of both single bacterial cells and human cancer cells. The obtained sequencing coverage rivals those of conventional techniques with superior sequence quality. In addition, we also demonstrate de novo assembly of uncultured soil bacteria and obtain draft genomes from single cell sequencing. This sd-MDA is promising for flexible and scalable use in single-cell sequencing.
Sequencing-based counting and size profiling of plasma Epstein–Barr virus DNA enhance population screening of nasopharyngeal carcinoma (2018)

Circulating tumor-derived DNA testing for cancer screening has recently been demonstrated in a prospective study on identification of nasopharyngeal carcinoma (NPC) among 20,174 asymptomatic individuals. Plasma EBV DNA, a marker for NPC, was detected using real-time PCR. While plasma EBV DNA was persistently detectable in 97.1% of the NPCs identified, ∼5% of the general population had transiently detectable plasma EBV DNA. We hypothesized that EBV DNA in plasma of subjects with or without NPC may have different molecular characteristics. We performed target-capture sequencing of plasma EBV DNA and identified differences in the abundance and size profiles of EBV DNA molecules within plasma of NPC and non-NPC subjects. NPC patients had significantly higher amounts of plasma EBV DNA, which showed longer fragment lengths. Cutoff values were established from an exploratory dataset and tested in a validation sample set. Adopting an algorithm that required a sample to concurrently pass cutoffs for EBV DNA counting and size measurements, NPCs were detected at a positive predictive value (PPV) of 19.6%. This represented superior performance compared with the PPV of 11.0% in the prospective screening study, which required participants with an initially detectable plasma EBV DNA result to be retested within 4 weeks. The observed differences in the molecular nature of EBV DNA molecules in plasma of subjects with or without NPC were successfully translated into a sequencing-based test that had a high PPV for NPC screening and achievable through single time-point testing.