gebhart/patrepeval huggingface dataset:
Nanoparticles Modified With Tumor-targeting scFv Deliver siRNA and miRNA for Cancer Therapy (2010)

Targeted delivery of RNA-based therapeutics for cancer therapy remains a challenge. We have developed a LPH (liposome-polycation-hyaluronic acid) nanoparticle formulation modified with tumor-targeting single-chain antibody fragment (scFv) for systemic delivery of small interfering RNA (siRNA) and microRNA (miRNA) into experimental lung metastasis of murine B16F10 melanoma. The siRNAs delivered by the scFv targeted nanoparticles efficiently downregulated the target genes (c-Myc/MDM2/VEGF) in the lung metastasis. Two daily intravenous injections of the combined siRNAs in the GC4-targeted nanoparticles significantly reduced the tumor load in the lung. miRNA-34a (miR-34a) induced apoptosis, inhibited survivin expression, and downregulated MAPK pathway in B16F10 cells. miR-34a delivered by the GC4-targeted nanoparticles significantly downregulated the survivin expression in the metastatic tumor and reduced tumor load in the lung. When miR-34a and siRNAs were co-formulated in GC4-targeted nanoparticles, an enhanced anticancer effect was observed.
Differentiation of a teratocarcinoma line: preferential development of cholinergic neurons. (1981)

A line of embryonal carcinoma cells, PCC7-S, established in vitro from a spontaneous testicular teratocarcinoma, has been studied. Upon removing the cells from a low density monolayer culture system and permitting the cells to form aggregates in suspension, we observed a change of several physical and biochemical parameters: (a) reduction in average cell volume, (b) blockage and accumulation of cells in G1, (c) rise in secreted protease activity, (d) rise in acetylcholinesterase and choline acetyltransferase activities, and (e) disappearance of embryonic antigen F9. Although PCC7 aggregates did not undergo substantial morphological changes while suspended, when aggregates 4 or more days old were allowed to attach to plastic tissue culture dishes, substantial neurite outgrowth occurred over the next 1-3 d. This process was markedly enhanced by the addition to the growth medium of carboxymethylcellulose and inhibitors of DNA synthesis. Transmission electron microscopy disclosed a neurite ultrastructure consistent with that of neuronal processes. A veratridine-stimulated, tetrodotoxin-blocked sodium influx of 100 nmol/min per mg protein was also observed in these differentiated surface cultures. This cell line is discussed in terms of its utility for the study of early events leading to a commitment to cellular differentiation, as well as for the investigation of terminal differentiation to cholinergic neurons.
Single-particle placement via self-limiting electrostatic gating (2008)

This letter reports single-particle placement in which exactly one nanoparticle is electrostatically guided and placed onto a target location. Using an ∼20 nm Au nanoparticle colloid as a model system, we demonstrate that self-limiting interactions between a charged nanoparticle and a charged substrate surface are extremely effective in positioning a single Au nanoparticle on each target location. Detailed theoretical calculations revealed that the self-limiting capability in the nanoparticle positioning is due to an increase in the free energy barrier after the first nanoparticle lands on a target position, effectively blocking the approach of other nanoparticles.
Ultrastructural evidence for communication between intramuscular vagal mechanoreceptors and interstitial cells of Cajal in the rat fundus (2007)

To assess whether afferent vagal intramuscular arrays (IMAs), putative gastrointestinal mechanoreceptors, form contacts with interstitial cells of Cajal of the intramuscular type (ICC-IM) and to describe any such contacts, electron microscopic analyses were performed on the external muscle layers of the fundus containing dextran-labelled diaminobenzidin (DAB)-stained IMAs. Special staining and embedding techniques were developed to preserve ultrastructural features. Within the muscle layers, IMA varicosities were observed in nerve bundles traversing major septa without contact with ICC-IM, contacting unlabelled neurites and glial cells. IMA varicosities were encountered in minor septa in contact with ICC-IM which were not necessarily in close contact with muscle cells. In addition, IMA varicosities were observed within muscle bundles in close contact with ICC-IM which were in gap junction contact with muscle cells. IMAs formed varicosities containing predominantly small agranular vesicles, occasionally large granular vesicles and prejunctional thickenings in apposition to ICC-IM processes, indicating communication between ICC and IMA via synapse-like contacts. Taken together, these different morphological features are consistent with a hypothesized mechanoreceptor role for IMA-ICC complexes. Intraganglionic laminar ending varicosities contacted neuronal somata and dendrites in the myenteric plexus of the fundus, but no contacts with ICC associated with Auerbach's plexus were encountered.
Evaluation of the hok/sok killer locus for enhanced plasmid stability (1994)

The effectiveness of the hok/sok plasmid stability locus and mechanism of cloned-gene loss was evaluated in shake-flask cultures. Addition of the hok/sok locus dramitically increasedapparent plasmid segregational stability to the hok/sok(-) control. In terms of the number of generations before 10%of the population became plasmid-free, segregational stability was increased by 11- to 20-fold in different media in the absence of induction of the cloned-gene (hok/sok(+) plasmid stable for over 200 generations in all media tested). With constant expression of beta-galactosidase in the absence of an tibiotic, the segregational stability of the plasmid containing hok/sok was incresed more than 17- to 30-fold when beta-galactosidase was expressed at 7-15 wt % of total cell protein. Although the hok/sok system stabilized the plasmid well infour different media (Luria-Bertani (LB), LB glucose, M9C Trp, and a representative fedbatch medium), the ability of hok/sok to maintain the plasmid with induction of the cloned gene decreased as the complexity of the media increased. This result is better interpreted in terms of the influence of cloned-gene expression on plasmidmaintenance; plasmid segregational stability decreased linearly as specificbeta-galactosidase activity increased. (c) 1994 John Wiley & Sons, Inc.
Middle Cerebral Artery Occlusion Suture Model for Mice (2008)

This chapter introduces the procedure, assessment, application, limitations, and technical considerations of the popular focal brain ischemia model in mice, the middle cerebral artery occlusion (MCAO) suture model. Preparation of the suture, surgical procedures, examination of neurological function, and infarct volume assessment are described in detail.
The Absence of IDO Upregulates Type I IFN Production, Resulting in Suppression of Viral Replication in the Retrovirus-Infected Mouse (2010)

Indoleamine 2,3-dioxygenase, the L-tryptophan-degrading enzyme, plays a key role in the powerful immunomodulatory effects on several different types of cells. Because modulation of IDO activities after viral infection may have great impact on disease progression, we investigated the role of IDO following infection with LP-BM5 murine leukemia virus. We found suppressed BM5 provirus copies and increased type I IFNs in the spleen from IDO knockout (IDO(-/-)) and 1-methyl-D-L-tryptophan-treated mice compared with those from wild-type (WT) mice. Additionally, the number of plasmacytoid dendritic cells in IDO(-/-) mice was higher in the former than in the WT mice. In addition, neutralization of type I IFNs in IDO(-/-) mice resulted in an increase in LP-BM5 viral replication. Moreover, the survival rate of IDO(-/-) mice or 1-methyl-D-L-tryptophan-treated mice infected with LP-BM5 alone or with both Toxoplasma gondii and LP-BM5 was clearly greater than the survival rate of WT mice. To our knowledge, the present study is the first report to observe suppressed virus replication with upregulated type I IFN in IDO(-/-) mice, suggesting that modulation of the IDO pathway may be an effective strategy for treatment of virus infection.
An attacker model for MANET routing security (2009)

Mobile ad-hoc networks are becoming ever more popular due to their flexibility, low cost, and ease of deployment. However, to achieve these benefits the network must employ a sophisticated routing protocol. Early proposed routing protocols were not designed to operate in the presence of attackers. There have been many subsequent attempts to secure these protocols, each with its own advantages and disadvantages. To allow for a comparison of these secure protocols, a single common attacker model is needed. Our first contribution in this work is to develop a comprehensive attacker model categorizing attackers based on their capabilities. This is in contrast to the existing models which seek to categorize attacks and then map that categorization back onto the attackers. Our second contribution is an analysis of the SAODV routing protocol using our new model, which demonstrates the structured approach inherent in our model and its benefits compared to existing work.
Context-aware query classification (2009)

Understanding users'search intent expressed through their search queries is crucial to Web search and online advertisement. Web query classification (QC) has been widely studied for this purpose. Most previous QC algorithms classify individual queries without considering their context information. However, as exemplified by the well-known example on query "jaguar", many Web queries are short and ambiguous, whose real meanings are uncertain without the context information. In this paper, we incorporate context information into the problem of query classification by using conditional random field (CRF) models. In our approach, we use neighboring queries and their corresponding clicked URLs (Web pages) in search sessions as the context information. We perform extensive experiments on real world search logs and validate the effectiveness and effciency of our approach. We show that we can improve the F1 score by 52% as compared to other state-of-the-art baselines.
LONG-TERM FOLLOW-UP FOR TYPE 1 (SUBRETINAL PIGMENT EPITHELIUM) NEOVASCULARIZATION USING A MODIFIED “TREAT AND EXTEND” DOSING REGIMEN OF INTRAVITREAL ANTIVASCULAR ENDOTHELIAL GROWTH FACTOR THERAPY (2010)

A modified "treat and extend" dosing regimen of intravitreal antivascular endothelial growth factor therapy reduces the need for monthly visits and imaging and allows for stable long-term visual acuity in eyes with type 1 neovascularization.
Chemically Synthesized Nanostructured VN for Pseudocapacitor Application (2005)

The objective of the present study is to synthesize high purity vanadium nitride (VN) nanocrystallites using a two-step ammonolysis of vanadium tetrachloride. VN crystallites were obtained at relatively low temperatures which exhibited a specific capacitance as high as by cyclic voltammetry. The electrochemical response of the nitride was evaluated at various scanning rates in 1 M KOH electrolyte. The nitride synthesized at different heat-treatment temperatures were further characterized by X-ray diffraction analysis, surface area analysis, and high-resolution transmission electron microscopy.
Molecular imaging of proteolytic activity in cancer (2003)

The early detection of both primary tumors and metastatic disease continue to be significant challenges in the diagnosis and staging of cancer. The growing recognition of the role of proteinases and proteolytic cascades in both the growth and metastasis of tumors has led to the development not only of therapeutic strategies using proteinase inhibitors, but also of methods to detect and image tumors in vivo via tumor-associated proteolytic activities. These imaging strategies derive from the enhanced sensitivity afforded by amplification that can be obtained by enzymatic processing to increase the efficacy of imaging "contrast agents" coupled with the inherent substrate specificity and selectivity of proteinases. This review describes key proteinases important in cancer progression, the strategies that have been devised to detect and image proteolytic activity in vivo, and the potential for this kind of functional imaging to serve as a marker for targeted therapy. The intent is to draw attention to the developing methods of molecular imaging to facilitate not only cancer diagnosis, but also for devising strategies for individualized targeted therapy and non-invasive monitoring of therapeutic efficacy.
Application of second generation advanced multimedia display processor (AMDP2) in a digital micro-mirror array based HDTV (2002)

A second generation of the advanced multimedia display processor (AMDPZ) is applied in a consumer multimedia HDTV prototype system. The AMDP2 provides a cost effective and flexible platform which can be used to implement a wide array of video processing algorithms. Examples include interlace to progressive scan conversion, image scaling, and picture enhancement. This paper describes a DLP/sup TM/ HDTV architecture and the application of the AMDPZ processor to perform video processing algorithms for various input signals for display on a 1280/spl times/720 digital micro-mirror device (DMD).
An amine-functionalized metal organic framework for preferential CO2 adsorption at low pressures (2009)

A metal organic framework with amine-lined pores gives high values for surface area and heat of adsorption with CO(2) gas.
Gene Therapy Targeting HIV Entry (2014)

Despite the unquestionable success of antiretroviral therapy (ART) in the treatment of HIV infection, the cost, need for daily adherence, and HIV-associated morbidities that persist despite ART all underscore the need to develop a cure for HIV. The cure achieved following an allogeneic hematopoietic stem cell transplant (HSCT) using HIV-resistant cells, and more recently, the report of short-term but sustained, ART-free control of HIV replication following allogeneic HSCT, using HIV susceptible cells, have served to both reignite interest in HIV cure research, and suggest potential mechanisms for a cure. In this review, we highlight some of the obstacles facing HIV cure research today, and explore the roles of gene therapy targeting HIV entry, and allogeneic stem cell transplantation in the development of strategies to cure HIV infection.
Effects of Constitutive Overexpression of Insulin-Like Growth Factor-1 on the Mechanical Characteristics and Molecular Properties of Ventricular Myocytes (1998)

Recently, insulin-like growth factor-1 (IGF-1) has been claimed to positively influence the cardiac performance of the decompensated heart. On this basis, the effects of constitutive overexpression of IGF-1 on the mechanical behavior of myocytes were examined in transgenic mice in which the cDNA for the human IGF-1B was placed under the control of a rat alpha-myosin heavy chain promoter. In mice heterozygous for the transgene and in nontransgenic littermates at 2.5 months of age, the alterations in Ca2+ sensitivity of tension development, unloaded shortening velocity, and sarcomere compliance were measured in skinned myocytes. The quantities and state of phosphorylation of myofilament proteins in these enzymatically dissociated ventricular myocytes were also examined. The overexpression of IGF-1 was characterized by a nearly 15% reduction in myofilament isometric tension at submaximum Ca2+ levels in the physiological range, whereas developed tension at maximum activation was unchanged. In contrast, unloaded velocity of shortening was increased 39% in myocytes from transgenic mice. Moreover, resting tension in these cells was reduced by 24% to 33%. Myocytes from nontransgenic mice pretreated with IGF-1 failed to reveal changes in myofilament Ca2+ sensitivity and unloaded velocity of shortening. The quantities of C protein, troponin I, and myosin light chain-2 were comparable in transgenic and nontransgenic mice, but their endogenous state of phosphorylation increased 117%, 100%, and 100%, respectively. Troponin T content was not altered, and myosin isozymes were essentially 100% V1 in both groups of mice. In conclusion, constitutive overexpression of IGF-1 may influence positively the performance of myocytes by enhancing shortening velocity and cellular compliance.
Cytotoxic T lymphocytes induced by liposomal antigens: mechanisms of immunological presentation. (1994)

It is known that liposomes can deliver encapsulated substances, including drugs and antigens, to lysosomes in macrophages. Because of this it has been assumed that although liposomes might be useful for induction of humoral (class II) immunity, they would not be capable of cytoplasmic delivery of antigen for introduction into the class I pathway leading to induction of cytotoxic T lymphocytes (CTLs). However, experiments conducted by numerous laboratories, including our own, have demonstrated the ability to induce CTLs either in vitro with cultured cells incubated with liposome-associated antigen, or in vivo after immunization of mice or monkeys with liposomes containing associated antigen. Using a monoclonal antibody that recognizes repeating sequences of tetrapeptide epitopes derived from the circumsporozoite protein of Plasmodium falciparum, it has been shown by immunogold electron microscopy that liposomal antigenic epitopes can actually spill from endosomes into the cytoplasm of cultured macrophages. On the basis of this observation, a theoretical intracellular pathway is proposed whereby liposomal antigen is processed by macrophages through a cytoplasmic process that results in delivery of antigenic epitopes to the Golgi apparatus and the endoplasmic reticulum. The liposomal antigenic epitopes would then have the opportunity to associate with class I MHC molecules and undergo vesicular transport to the surface of the cells for presentation and induction of CTLs.
Topically administered immunoglobulin reduces pulmonary respiratory syncytial virus shedding in owl monkeys (1988)

A human intravenous immunoglobulin preparation containing neutralizing antibodies to respiratory syncytial virus (RSV) was utilized for intratracheal and topical treatment of laboratory-induced RSV infections in owl monkeys (Aotus trivirgatus). Topically administered antibodies induced significant reductions in RSV shedding in the lower respiratory tract.
Pegylation of Interferon Alfa: Structural and Pharmacokinetic Properties (2003)

The attachment of a polyethylene glycol (PEG) polymer to a protein or peptide is becoming increasingly common within the pharmaceutical industry as a way of altering the activity of the parent molecule. Significant improvements in biological activity with PEG molecules have been seen with several licensed drugs, allowing for product life cycle management, as well as with experimental compounds in development that have pharmaceutical properties making them suitable candidates for pegylation. Among the various disease states that have been targeted for the study of drugs incorporating pegylation technology, the treatment of chronic hepatitis C with interferon-based compounds offers significant potential for clinical impact. Two separate compounds, peginterferon alfa-2a (PEGASYS) and peginterferon alfa-2b (PEG-Intron) are now both approved for use alone and in combination with ribavirin for the treatment of chronic hepatitis C. However, the different PEG moieties attached to the native protein, the site of attachment and the type of bond involved lead to vast differences with respect to the pharmacokinetics (including absorption, biodistribution, metabolism and elimination) and pharmacodynamics of these two compounds. This article discusses the differences that exist between these compounds, which may lead to different clinical profiles for their use in the treatment of patients with hepatitis C.
Topology analysis of software dependencies (2008)

Before performing a modification task, a developer usually has to investigate the source code of a system to understand how to carry out the task. Discovering the code relevant to a change task is costly because it is a human activity whose success depends on a large number of unpredictable factors, such as intuition and luck. Although studies have shown that effective developers tend to explore a program by following structural dependencies, no methodology is available to guide their navigation through the thousands of dependency paths found in a nontrivial program. We describe a technique to automatically propose and rank program elements that are potentially interesting to a developer investigating source code. Our technique is based on an analysis of the topology of structural dependencies in a program. It takes as input a set of program elements of interest to a developer and produces a fuzzy set describing other elements of potential interest. Empirical evaluation of our technique indicates that it can help developers quickly select program elements worthy of investigation while avoiding less interesting ones.
Expression and diagnostic utility of hepatitis E virus putative structural proteins expressed in insect cells (1993)

The full-length putative structural proteins encoded by open reading frame 2 (ORF2) and ORF3 of hepatitis E virus have been cloned and expressed in recombinant baculovirus. Sera obtained from 28 Sudanese pediatric patients with acute hepatitis and 19 pediatric control patients were analyzed for reactivity to hepatitis E virus by using the baculovirus-expressed ORF2 and ORF3 proteins in a Western blot (immunoblot) format. Seventeen of the 18 patients classified as having non-A, non-B hepatitis, without acute antibody markers for hepatitis A, B, or C viruses, Epstein-Barr virus, or cytomegalovirus, were shown to have immunoglobulin M (IgM) antibodies to the recombinant ORF2 protein, as did two patients with chronic hepatitis B, three of seven patients with acute hepatitis A, and one patient with acute hepatitis B. None of the 19 control patients had IgM antibodies against the ORF2 or ORF3 proteins. The Western blot assay using the baculovirus-expressed ORF3 protein did not appear to be as sensitive as the assay based on the ORF2 protein. Only 10 of the patients classified as having non-A, non-B hepatitis had IgM antibodies to the baculovirus-expressed ORF3 protein. We conclude that a Western blot assay which uses a baculovirus-expressed ORF2 protein is both sensitive and specific for diagnosing acute hepatitis E.
Pyrolysis of Kraft Lignin with Additives (2011)

The pyrolysis of softwood (SW) kraft lignin in the presence of NiCl2 and ZSM-5 zeolite as an additive was examined at 700 °C. Gel permeation chromatography (GPC), quantitative 13C and 31P NMR were used to characterize the pyrolysis oil. Based on the results of 13C and 31P NMR for the pyrolysis oils, the use of zeolite during pyrolysis caused the near complete loss of aliphatic hydroxyl and carboxyl groups in the bio-oil and about 80% of methoxyl groups were also eliminated. The zeolite was shown to improve the decomposition of aliphatic hydroxyl groups, carboxyl, methoxyl groups, and ether bonds in the lignin during pyrolysis. In addition, as determined by 13C NMR, the oxygen content in the bio-oil decreased after the use of zeolite. The results of GPC analysis indicated that the addition of H-ZSM-5 zeolite with lignin provided a bio-oil that had ∼10% lower average molecular weight than the pyrolysis product acquired without the additive.