gebhart/patrepeval huggingface dataset:
Conjugates of Oligonucleotides and Analogues with Cell Penetrating Peptides as Gene Silencing Agents (2005)

The review describes key aspects of the synthesis and biological activities of conjugates of oligonucleotides and their analogues with synthetic peptides, in particular aimed towards gene silencing applications. The common methods of synthesis of oligonucleotide-peptide conjugates (OPCs) and PNA-peptide conjugates (PPCs) are described, which include both total solid-phase and fragment coupling approaches. In addition, various applications of conjugates as gene silencing agents are outlined. These include antisense and steric block applications in mammalian cells of OPCs, PPCs and phosphorodiamidate morpholinooligonucleotide (PMO)-peptide conjugates, gene silencing in bacteria, various DNA targeting applications, and recent reports of gene silencing activities of siRNA-peptide conjugates. A table listing all peptides used as oligonucleotide conjugates for gene silencing applications is also included.
Bone Marrow Transplantation and Cataract Development (1993)

Posterior subcapsular cataract following BMT is uncommon and rarely requires surgery. Total dose and duration of corticosteroid therapy are the most important risk factors for development of cataract, but total body irradiation is not a statistically significant risk factor.
Aggregating local descriptors into a compact image representation (2010)

We address the problem of image search on a very large scale, where three constraints have to be considered jointly: the accuracy of the search, its efficiency, and the memory usage of the representation. We first propose a simple yet efficient way of aggregating local image descriptors into a vector of limited dimension, which can be viewed as a simplification of the Fisher kernel representation. We then show how to jointly optimize the dimension reduction and the indexing algorithm, so that it best preserves the quality of vector comparison. The evaluation shows that our approach significantly outperforms the state of the art: the search accuracy is comparable to the bag-of-features approach for an image representation that fits in 20 bytes. Searching a 10 million image dataset takes about 50ms.
Targeted Disruption of the NIT8 Gene in Chlamydomonas reinhardtii (1995)

We have used homologous recombination to disrupt the nuclear gene NIT8 in Chlamydomonas reinhardtii. This is the first report of targeted gene disruption of an endogenous locus in C. reinhardtii and only the second for a photosynthetic eukaryote. NIT8 encodes a protein necessary for nitrate and nitrite assimilation by C. reinhardtii. A disruption vector was constructed by placing the CRY1-1 selectable marker gene, which confers emetine resistance, within the NIT8 coding region. nit8 mutants are unable to grow on nitrate as their sole nitrogen source (Nit-) and are resistant to killing by chlorate. One of 2,000 transformants obtained after selection on emetine-chlorate medium contained a homologous insertion of five copies of the disruption plasmid into the NIT8 gene, producing an emetine-resistant, chlorate-resistant Nit- phenotype. The mutant phenotype was rescued by the wild-type NIT8 gene upon transformation. Seven other mutations at the nit8 locus, presumably resulting from homologous recombination with the disruption plasmid, were identified but were shown to be accompanied by deletions of the surrounding genomic region.
Ribosomal Proteins and Colorectal Cancer (2007)

The ribosome is essential for protein synthesis. The composition and structure of ribosomes from several organisms have been determined, and it is well documented that ribosomal RNAs (rRNAs) and ribosomal proteins (RPs) constitute this important organelle. Many RPs also fill various roles that are independent of protein biosynthesis, called extraribosomal functions. These functions include DNA replication, transcription and repair, RNA splicing and modification, cell growth and proliferation, regulation of apoptosis and development, and cellular transformation. Previous investigations have revealed that RP regulation in colorectal carcinomas (CRC) differs from that found in colorectal adenoma or normal mucosa, with some RPs being up-regulated while others are down-regulated. The expression patterns of RPs are associated with the differentiation, progression or metastasis of CRC. Additionally, the recent literature has shown that the perturbation of specific RPs may promote certain genetic diseases and tumorigenesis. Because of the implications of RPs in disease, especially malignancy, our review sought to address several questions. Why do expression levels or categories of RPs differ in different diseases, most notably in CRC? Is this a cause or consequence of the diseases? What are their possible roles in the diseases? We review the known extraribosomal functions of RPs and associated changes in colorectal cancer and attempt to clarify the possible roles of RPs in colonic malignancy.
LAT1 expression is closely associated with hypoxic markers and mTOR in resected non-small cell lung cancer. (2011)

LAT1 expression is closely correlated with hypoxic markers and mTOR pathway in patients with resected NSCLC.
Compact Reverse Water-Gas-Shift Reactor for Extraterrestrial In Situ Resource Utilization (2008)

A compact reverse water-gas-shift reactor suitable for extraterrestrial use as part of the in situ propellant production system is reported. The reactor is less than 15 cm 3 in volume and weighs less than 50 g. With an Ru/ZrO 2 -CeO catalyst it produces over 150 g H 2 O/h operating at 800°C. This is near equilibrium conversion at about half-scale of a Mars sample-return mission. Even at these high processing rates, the pressure drop remains low (from 1.6 to 7.6 kPa).
A Plasmid-Based Self-Amplifying Sindbis Virus Vector (1995)

Sindbis virus was used as a self-amplifying eukaryotic expression vector. A recombinant cDNA genome of this (+)-strand RNA virus was placed under the transcriptional control of a Rous sarcoma virus LTR (RSV) promoter. Transfection of this plasmid construct into mammalian cell lines (3T3, HepG2, and 293 cells) resulted in expression of the luciferase reporter gene. High-expression levels were also measured after transfection into primary rat myoblasts. In differentiated myotubes, expression levels generated by the Sindbis virus vector were up to 200 times higher than those obtained with a conventional RSV expression vector. In vivo expression was detected after injection of plasmid DNA into mouse quadriceps. In vivo expression was transient and undetectable by day 16. This self-amplifying expression vector can be used for generating high-level expression of transgenes in vitro and in vivo. Its transient nature in vivo could allow for safe, short-term delivery of gene products in gene therapy protocols. It should facilitate the study of Sindbis and other RNA viruses.
Human Coronavirus and Acute Respiratory Illness in Older Adults with Chronic Obstructive Pulmonary Disease (2009)

The frequencies of HCoV and LDI illnesses were similar. HCoV illness was less severe than LDI illness, was accompanied by multiple respiratory and systemic symptoms, and was associated with hospitalization.
High speed, wide velocity dynamic range Doppler optical coherence tomography (Part III): in vivo endoscopic imaging of blood flow in the rat and human gastrointestinal tracts (2003)

We previously described a fiber based Doppler optical coherence tomography system [1] capable of imaging embryo cardiac blood flow at 4~16 frames per second with wide velocity dynamic range [2]. Coupling this system to a linear scanning fiber optical catheter design that minimizes friction and vibrations, we report here the initial results of in vivo endoscopic Doppler optical coherence tomography (EDOCT) imaging in normal rat and human esophagus. Microvascular flow in blood vessels less than 100 microm diameter was detected using a combination of color-Doppler and velocity variance imaging modes, during clinical endoscopy using a mobile EDOCT system.
Interferon β-1a in ulcerative colitis: a placebo controlled, randomised, dose escalating study (2003)

IFN-beta-1a may represent a promising novel treatment approach in ulcerative colitis.
Field emission from p-type polycrystalline diamond films (1995)

Vapor-deposited-diamond field emitters are fabricated using diamond film technology compatible with integrated circuit processing. The field emission data from p-type polycrystalline diamond films are presented. Field emission current in the range of 15 μA was detected at an electric field intensity of &amp;lt;20 MV/m at a pressure of 10−7 Torr. A current of approximately 50 nA was observed at a pressure up to 10−2 Torr in H2 environment.
Spring Switchgrass Harvest with a New Holland Large Square Baler (2010)

A New Holland BB9080 large square baler was used to produce large square bales of switchgrass with 900mm by 1200mm end dimensions. The switchgrass was harvested for seed in the fall and the biomass was left to overwinter on the ground. Bales of two different densities were produced and weighed in order to study the densification capabilities of the baler. Fuel consumption data and GPS data were also collected during bale production. The baler had the capability of producing switchgrass bales that approached 200 kg/m3 at 12.5% (wb) moisture content. Fuel consumption during the baling process varied from one to two liters of diesel fuel per Mg of switchgrass baled. The baler was towed at varying speeds in order to feed the baler at a constant rate. Therefore heavier windrows resulted in lower ground speeds. The most significant finding was the dramatic increase in the efficiency of bale production due to increased windrow density and decreased ground speed of the tractor and baler. There was a 31% decrease in fuel consumption in terms of L/Mg of switchgrass baled due to decreasing the ground speed from 7.45 km/h to 5.29 km/h.
Electroluminescence from Well-Defined Tetrahedral Oligophenylenevinylene Tetramers (2000)

Organic light-emitting diodes (LEDs) with small turn-on voltages are fabricated here using molecules based on the tetrakis(4-styryldistyrylbenzene)methane framework (see Figure). The synthesis of these molecules is reported, their absorption and luminescence properties are compared, and the effect of device architecture on performance is investigated.
Sleep-Disordered Breathing and Poor Functional Outcome After Stroke (1996)

SDB accompanied by arterial oxyhemoglobin desaturation is common in patients undergoing rehabilitation after stroke and is associated with higher mortality at 1 year and lower BI scores at discharge and at 3 and 12 months after stroke. SDB may be an independent predictor of worse functional outcome. Obstructive sleep apnea appeared to be the most common form of SDB, and the frequent history of snoring suggests that SDB preceded the stroke in most patients.
Catecholamines Regulate the Activity, Secretion, and Synthesis of Renalase (2008)

These data identify a novel mechanism for the regulation of circulating catecholamines. In the renalase pathway, excess catecholamine facilitates the conversion of prorenalase, an inactive plasma amine oxidase, to renalase, which can degrade catecholamines. Excess catecholamines not only regulate the activation of prorenalase but also promote its secretion and synthesis. Because chronic kidney disease is associated with a number of systemic abnormalities, including activation of the sympathetic nervous system, increased catecholamines levels, cardiac hypertrophy, and hypertension, renalase replacement is an attractive therapeutic modality owing to its role in catecholamine metabolism.
Pancreatic Ductal Adenocarcinoma: Current and Evolving Therapies (2017)

Pancreatic ductal adenocarcinoma (PDAC), which constitutes 90% of pancreatic cancers, is the fourth leading cause of cancer-related deaths in the world. Due to the broad heterogeneity of genetic mutations and dense stromal environment, PDAC belongs to one of the most chemoresistant cancers. Most of the available treatments are palliative, with the objective of relieving disease-related symptoms and prolonging survival. Currently, available therapeutic options are surgery, radiation, chemotherapy, immunotherapy, and use of targeted drugs. However, thus far, therapies targeting cancer-associated molecular pathways have not given satisfactory results; this is due in part to the rapid upregulation of compensatory alternative pathways as well as dense desmoplastic reaction. In this review, we summarize currently available therapies and clinical trials, directed towards a plethora of pathways and components dysregulated during PDAC carcinogenesis. Emerging trends towards targeted therapies as the most promising approach will also be discussed.
Autoradiographic localization of angiotensin II receptors in rat brain. (1984)

The 125I-labeled agonist analog [1-sarcosine]-angiotensin II ( [Sar1]AII) bound with high specificity and affinity (Ka = 2 X 10(9) M-1) to a single class of receptor sites in rat brain. This ligand was used to analyze the distribution of AII receptors in rat brain by in vitro autoradiography followed by computerized densitometry and color coding. A very high density of AII receptors was found in the subfornical organ, paraventricular and periventricular nuclei of the hypothalamus, nucleus of the tractus solitarius, and area postrema. A high concentration of receptors was found in the suprachiasmatic nucleus of the hypothalamus, lateral olfactory tracts, nuclei of the accessory and lateral olfactory tracts, triangular septal nucleus, subthalamic nucleus, locus coeruleus, and inferior olivary nuclei. Moderate receptor concentrations were found in the organum vasculosum of the lamina terminalis, median preoptic nucleus, medial habenular nucleus, lateral septum, ventroposterior thalamic nucleus, median eminence, medial geniculate nucleus, superior colliculus, subiculum, pre- and parasubiculum, and spinal trigeminal tract. Low concentrations of sites were seen in caudate-putamen, nucleus accumbens, amygdala, and gray matter of the spinal cord. These studies have demonstrated that AII receptors are distributed in a highly characteristic anatomical pattern in the brain. The high concentrations of AII receptors at numerous physiologically relevant sites are consistent with the emerging evidence for multiple roles of AII as a neuropeptide in the central nervous system.
Critical Observations on the Neurotoxicity of Silver (2007)

Silver is a xenobiotic element with no recognized trace metal value in the human body. It is absorbed into the body through the lungs, gastrointestinal tract, mucus membranes of the urinogenital tract, and through the skin, mainly in the form of silver protein complexes. Although silver is metabolized throughout the soft tissues, available evidence from experimental animal studies and human clinical reports has failed to unequivocally establish that it enters tissues of the central nervous system or is a cause of neurotoxic damage. Argyria characterized by deposition of particles of silver sulfide or silver selenide is the principle contraindication for using silver in medical devices or occupationally. This presents discoloration of the skin but is not regarded as a health risk or manifestation of toxicity. No evidence is available to demonstrate the toxic risk of silver to the peripheral nervous system, although silver sulfide deposits have been identified in the region of cutaneous nerves. Transitory silver sulfide deposits seen in the tissues of the blood-brain and blood-CSF barriers are mostly lysosomally bound or deposited on basement membranes or collagen without toxic effect. Silver is mostly excreted from the body in the urine and feces. Further research is indicated to evaluate the role of metal binding proteins including metallothioneins as cytoprotectants for neurological tissue.
An ontology-based knowledge base for the representation and reuse of software patterns (2006)

The description, localization and effective reuse of software patterns and systems of patterns can be approached through an ontology-based formalism. An ontology is an explicit specification of objects, concepts and entities of an area of interest, besides the relationships between these concepts expressed through axioms. This work introduces ONTOPATTERN, an ontology that represents knowledge about how patterns are described and about their relationships in a pattern system. Patterns are included as instances of classes in the ontology, thus turning ONTOPATTERN a knowledge base where concepts are semantically related and where searches and inferences can be made thus facilitating the understanding and reuse of patterns. The use of ONTOPATTERN is illustrated through an example on the construction of a multi-agent framework.
Mechanisms of Growth Control of Kaposi's Sarcoma–Associated Herpes Virus–Associated Primary Effusion Lymphoma Cells (1998)

Primary effusion lymphoma (PEL) is a distinct clinicopathologic entity associated with Kaposi's sarcoma-associated herpes virus (KSHV). Several cytokines, including interleukin-6 (IL-6), basic fibroblast growth factor (bFGF), and platelet-derived growth factor (PDGF) may be important for survival of KS cells. However, little is known about the interaction of cytokines with KSHV-infected lymphocytes from PEL. Therefore, we investigated what cytokines were produced by KSHV-infected PEL cell lines (KS-1, BC-1, BC-2), what cytokine receptors were expressed by these cells, what response these cells had to selected cytokines, and what was the effect of IL-6 antisense phosphorothioated oligonucleotides. Reverse transcriptase-polymerase chain reaction (RT-PCR) and protein studies showed that these three cell lines produced IL-10, IL-6, and the receptors for IL-6. The granulocyte macrophage colony-stimulating factor (GM-CSF), IL-1β, IL-8, IL-12, bFGF, PDGF, and c-kit transcripts were not detected in the cell lines. High levels (0.7 to 5 ng/mL/106cells/48 hours) of IL-6 protein were consistently detected in supernatants of the cell lines by enzyme-linked immunosorbent assay (ELISA) tests. In clonogenic assays, interferon-α (IFN-α) and IFN-γ suppressed the clonal growth of the PEL cells, but GM-CSF, IL-4, IL-6, IL-8, IL-10, and oncostatin M did not change it. We examined for several autocrine loops that have been suggested to occur in KS. Experiments using antisense oligonucleotides showed that the clonal growth of KS-1 and BC-1 was nearly 100% inhibited by IL-6 antisense oligonucleotides (10 μmol/L), but not at all by either oligonucleotides (≤10 μmol/L) to IL-6 sense, IL-6 scrambled, viral IL-6 (vIL-6) antisense, or IL-10 antisense. Furthermore, the IL-6 antisense oligonucleotides had no effect on two B-cell lymphoma cell lines, which were not infected with KSHV. Addition of IL-6 antibody did not inhibit clonal growth of any of the cell lines. Taken together, we have defined the cytokines and their receptors expressed on PEL cells and have found that these cells synthesized IL-6 and IL-6 receptors; interruption of this pathway by IL-6 antisense oligonucleotides specifically prevented the growth of these cells. These findings will offer potential new therapeutic strategies for PEL.
DNA binding analysis of glucocorticoid receptor specificity mutants (1992)

The glucocorticoid receptor (GR) DNA binding domain consists of several conserved amino acids and folds into two zinc finger-like structures. Previous transactivation experiments indicated that three amino acids residing in this region, Gly, Ser and Val, appear to be critical for target-site discrimination. Based on the solved crystal structure, these residues are at the beginning of an amphipathic alpha-helix that interacts with the DNA's major groove; of these, only valine, however, contacts DNA. In order to examine their functional role directly, we have substituted these residues for the corresponding amino acids from the estrogen receptor (ER), overexpressed and purified the mutant proteins, and assayed their binding specificity and affinity by gel mobility shifts using glucocorticoid or estrogen response elements (GRE or ERE, respectively) as DNA probes. We find that all three residues are indeed required to fully switch GR's specificity to an ERE. The contacting valine in GR is of primary importance. The corresponding residue in ER, alanine, is less important for specificity, while glutamic acid, four amino acids towards the N-terminus, is most critical for ER discrimination. Finally, we show that the GR DNA binding domain carrying all three ER-specific mutations has a significantly higher affinity for an ERE than the ER DNA binding domain itself. We interpret these results in the context of both the data presented here and the crystal structure of the GR DNA binding domain complexed to a GRE.
Human MUC1 Carcinoma Antigen Regulates Intracellular Oxidant Levels and the Apoptotic Response to Oxidative Stress (2003)

The DF3/MUC1 transmembrane oncoprotein is aberrantly overexpressed by most human carcinomas. Certain insights are available regarding a role for MUC1 in intracellular signaling; however, no precise function has been ascribed to this molecule. The present results demonstrate that MUC1 expression is up-regulated by oxidative stress and that this response is mediated by activation of MUC1 gene transcription. A role for MUC1 in the oxidative stress response is supported by the demonstration that MUC1 expression is associated with attenuation of endogenous and H2O2-induced intracellular levels of reactive oxygen species (ROS). MUC1-dependent regulation of ROS is mediated at least in part by up-regulation of anti-oxidant enzyme (superoxide dismutase, catalase, and glutathione peroxidase) expression. In concert with these findings, we show that the apoptotic response to oxidative stress is attenuated by a MUC1-dependent mechanism. These results support a model in which activation of MUC1 by oxidative stress provides a protective function against increased intracellular oxidant levels and ROS-induced apoptosis.