gebhart/patrepeval huggingface dataset:
Highly versatile SPION encapsulated PLGA nanoparticles as photothermal ablators of cancer cells and as multimodal imaging agents (2017)

We have designed versatile polymeric nanoparticles with cancer cell specific targeting capabilities via aptamer conjugation after the successful encapsulation of curcumin and superparamagnetic iron oxide nanoparticles (SPIONs) inside a PLGA nanocapsule. These targeted nanocomposites were selectively taken up by tumor cells, under in vitro conditions, demonstrating the effectiveness of the aptamer targeting mechanism. Moreover, the nanocomposite potentially functioned as efficient multiprobes for optical, magnetic resonance imaging (MRI) and photoacoustic imaging contrast agents in the field of cancer diagnostics. The hyperthermic ability of these nanocomposites was mediated by SPIONs upon NIR-laser irradiation. In vitro cytotoxicity was shown by curcumin-loaded nanoparticles as well as the photothermal ablation of cancer cells mediated by the drug-encapsulated nanocomposite demonstrated the potential therapeutic effect of the nanocomposite. In short, we portray the aptamer-conjugated nanocomposite as a multimodal material capable of serving as a contrast agent for MR, photoacoustic and optical imaging. Furthermore, the nanocomposite functions as a targetable drug nanocarrier and a NIR-laser inducible hyperthermic material that is capable of ablating PANC-1 and MIA PaCa-2 cancer cell lines.
Spontaneous and restriction enzyme-induced chromosomal recombination in mammalian cells. (1994)

We have derived Chinese hamster ovary (CHO) cell hybrids containing herpes simplex virus thymidine kinase (tk) heteroalleles for the study of spontaneous and restriction enzyme-induced interchromosomal recombination. These lines allowed us to make a direct comparison between spontaneous intrachromosomal and interchromosomal recombination using the same tk heteroalleles at the same genomic insertion site. We find that the frequency of interchromosomal recombination is less by a factor of at least 5000 than that of intrachromosomal recombination. Our results with mammalian cells differ markedly from results with Saccharomyces cerevisiae, with which similar studies typically give only a 10-to 30-fold difference. Next, to inquire into the fate of double-strand breaks at either of the two different Xho I linker insertion mutations, we electroporated PaeR7I enzyme, an isoschizomer of Xho I, into these hybrids. A priori, these breaks can be repaired either by recombination from the homology or by end-joining. Despite a predicted bias against recovering end-joining products in our system, all cells characterized by enzyme-induced resistance to hypoxanthine/aminopterin/thymidine were, in fact, due to nonhomologous recombination or end-joining. These results are in agreement with other studies that used extrachromosomal sequences to examine the relative efficiencies of end-joining and homologous recombination in mammalian cells, but are in sharp contrast to results of analogous studies in S. cerevisiae, wherein only products of homologous events are detected.
Gen-Probe Rapid Diagnostic System for the Mycobacterium avium complex does not distinguish between Mycobacterium avium and Mycobacterium paratuberculosis (1991)

Three reference and 16 field strains of Mycobacterium paratuberculosis were tested with the Gen-Probe Mycobacterium avium complex DNA probe (Gen-Probe Inc., San Diego, Calif.). All reference strains and 12 of 16 field strains gave positive hybridization results with the probe. This study shows that the M. avium complex probe does not distinguish between M. avium and M. paratuberculosis and indicates heterogeneity in the 16S rRNA gene of M. paratuberculosis.
Low-Level Vagosympathetic Stimulation (2009)

LL-VNS may prevent episodic AF caused by rapid PV and non-PV firing.
Emerging Infectious Diseases: a 10-Year Perspective from the National Institute of Allergy and Infectious Diseases (2005)

Although optimists once imagined that serious infectious disease threats would by now be conquered, newly emerging (e.g., severe acute respiratory syndrome [SARS]), reemerging (e.g., West Nile virus), and even deliberately disseminated infectious diseases (e.g., anthrax bioterrorism) continue to appear throughout the world. Over the past decade, the global effort to identify and characterize infectious agents, decipher the underlying pathways by which they cause disease, and develop preventive measures and treatments for many of the world's most dangerous pathogens has resulted in considerable progress. Intramural and extramural investigators supported by the National Institute of Allergy and Infectious Diseases (NIAID) have contributed substantially to this effort. This overview highlights selected NIAID-sponsored research advances over the past decade, with a focus on progress in combating HIV/AIDS, malaria, tuberculosis, influenza, SARS, West Nile virus, and potential bioterror agents. Many basic research discoveries have been translated into novel diagnostics, antiviral and antimicrobial compounds, and vaccines, often with extraordinary speed.
Filling of poly(lactic acid) with native starch (1996)

Abstract Poly(lactic‐acid) (PLA), a biodegradable polyester with excellent properties for different polymer applications, will play a major role in future markets for biodegradable polymers. But only if the currently very high price level can be reduced significantly to at least 4 $US/kg. Therefore, studies to fill poly(lactic acid) (PLA) with relative inexpensive native corn starch were conducted. Because PLA is a very brittle material with a glass transition point at 54°C, filling of PLA with native starch might seem unrealistic, as the brittleness is increased by the dispersed starch granules. To avoid this, low molecular weight poly(ethylene glycol) (PEG) is introduced into the PLA to enhance crystallization and to lower the glass transition temperature significantly under possible usage temperatures. The polymer that is modified in this way is then filled with native starch. The thermal behavior of the achieved di‐ or triblends is determined by means of differential scanning calorimetry (DSC) and the degradation behavior at high temperature has been looked at with the help of thermogravimetric analysis (TGA).
CNP is present in canine renal tubular cells and secreted by cultured opossum kidney cells (1994)

C-type natriuretic peptide (CNP) is a vasoactive and antimitogenic peptide that is structurally similar but genetically distinct from atrial natriuretic peptide. While first discovered in the brain, CNP has been shown to be produced by endothelial cells and may function in a paracrine and autocrine fashion in the control of vascular tone. Recently, CNP immunoreactivity and B-type natriuretic peptide receptors (NPR-B), for which CNP is a specific ligand, have been identified in the kidney. The present study was designed to determine whether renal epithelial cells produce and secrete CNP and whether CNP immunoreactivity is present in canine kidney. Opossum kidney (OK) cells that express proximal tubular cell characteristics were incubated for 6 h in fetal calf serum-free Dulbecco's modified Eagle's medium (DMEM). CNP immunoreactivity was measured in the preincubation and 6-h conditioned media by radioimmunoassay (RIA) using a specific antibody to CNP-22. Furthermore the molecular form of this CNP-like protein was determined by reverse-phase high-performance liquid chromatography (HPLC), and intracellular localization of the CNP immunoreactivity was determined by immunohistochemical staining. CNP immunoreactivity was also determined in renal tissue from dogs subjected to saline or endothelin infusion. Six-hour incubation in DMEM resulted in accumulation of CNP immunoreactivity (baseline below detection level vs. 6 h = 117.3 +/- 8.3 pg/ml, P < 0.001). Intracellular CNP concentration determined after sonication was 1.9 +/- 0.2 micrograms/g protein, and immunohistochemical staining for CNP was markedly positive in the cytoplasm.(ABSTRACT TRUNCATED AT 250 WORDS)
Uniform Resampling of Digitized Contours (1985)

This paper addresses the problem of the nonuniform intersample distance of digital curves obtained as a result of quantization of continuous contours on a square lattice. A resampling algorithm based on variable-factor interpolation and decimation is presented, and its performance is evaluated analytically and by computer simulations assuming the grid-intersect quantization. It is shown that the output of the resampling algorithm outperforms the original digital curve in terms of the average and maximum error in the measurement of length by 50 and 73 percent, respectively. The resampling algorithm can be used as a preprocessing stage in shape analysis systems to enhance their performance by increasing the accuracy and consistency of both local and global features such as curvature and the Fourier shape descriptors.
ATRA-induced upregulation of Beclin 1 prolongs the life span of differentiated acute promyelocytic leukemia cells (2011)

Acute promyelocytic leukemia (APL) results from a blockade of granulocyte differentiation at the promyelocytic stage. All-trans retinoic acid (ATRA) induces clinical remission in APL patients by enhancing the rapid differentiation of APL cells and the clearance of PML-RARα, APL's hallmark oncoprotein. In the present study, we demonstrated that both autophagy and Beclin 1, an autophagic protein, are upregulated during the course of ATRA-induced neutrophil/granulocyte differentiation of an APL-derived cell line named NB4 cells. This induction of autophagy is associated with downregulation of Bcl-2 and inhibition of mTOR activity. Small interfering RNA-mediated knockdown of BECN1 expression enhances apoptosis triggered by ATRA in NB4 cells but does not affect the differentiation process. These results provide evidence that the upregulation of Beclin 1 by ATRA constitutes an anti-apoptotic signal for maintaining the viability of mature APL cells, but has no crucial effect on the granulocytic differentiation. This finding may help to elucidate the mechanisms involved in ATRA resistance of APL patients, and in the ATRA syndrome caused by an accumulation of mature APL cells.
Circulating Tumor DNA Analysis in Patients With Cancer: American Society of Clinical Oncology and College of American Pathologists Joint Review (2018)

The evidence indicates that testing for ctDNA is optimally performed on plasma collected in cell stabilization or EDTA tubes, with EDTA tubes processed within 6 hours of collection. Some ctDNA assays have demonstrated clinical validity and utility with certain types of advanced cancer; however, there is insufficient evidence of clinical validity and utility for the majority of ctDNA assays in advanced cancer. Evidence shows discordance between the results of ctDNA assays and genotyping tumor specimens, and supports tumor tissue genotyping to confirm undetected results from ctDNA tests. There is no evidence of clinical utility and little evidence of clinical validity of ctDNA assays in early-stage cancer, treatment monitoring, or residual disease detection. There is no evidence of clinical validity or clinical utility to suggest that ctDNA assays are useful for cancer screening, outside of a clinical trial. Given the rapid pace of research, reevaluation of the literature will shortly be required, along with the development of tools and guidance for clinical practice.
Expression of bone morphogenetic protein‐7 (BMP‐7) in human prostate (2004)

It has been reported that the BMP-7 mRNA level is androgen-dependent in the mouse prostate. The present results suggest that the BMP-7 mRNA level is androgen-dependent in the human prostate, since the expression of BMP-7 was decreased in local recurrent prostate cancer tissues after hormonal therapy and was increased by DHT.
Objective evaluation of the sweet spot size in spatial sound reproduction using elevated loudspeakers (2010)

In a previous study, three crosstalk cancellation techniques were evaluated and compared under different conditions. Least-squares approximations in the frequency and time domain were evaluated along with a method based on minimum-phase decomposition and a frequency independent delay. In general, the least-squares methods outperformed the method based on the minimum-phase decomposition. However, the evaluation was only done for the best-case scenario, where the transfer functions used to design the filters correspond to the listener's transfer functions and his/her location and orientation relative to the loudspeakers. This paper presents a follow-up evaluation of the performance of the three inversion techniques when the above mentioned conditions are relaxed. A setup to measure the sweet spot of different loudspeaker arrangements is described. The sweet spot was measured for 21 different loudspeaker configurations, including two- and four-channel setups. Lateral and frontal displacement were measured along with head rotations. The setups were evaluated at different elevation angles. The results suggest that when the loudspeakers are placed at elevated positions, a wider effective area is obtained. Additionally, the two-channel configurations showed to be more robust to head misalignments than the four-channel configurations.
Some Current Ideas on the Pathogenesis and the Role of Neuroprotection in Glaucomatous Optic Neuropathy (2003)

The primary features of glaucomatous optic neuropathy are characteristic changes in the optic nerve head, a decrease in number of surviving ganglion cells and a reduction in vision. It is now generally accepted that a number of factors, including elevated intraocular pressure, could lead to the changes seen in the optic nerve head and to obtain a pharmacological means to treat the causes will vary from patient to patient. In contrast, a cascade of events have been proposed to explain how the changes in the optic nerve head may lead to the slow and differential death of ganglion cells in the disease. It is also proposed that drugs (neuroprotectants) influencing this cascade of events can attenuate ganglion cell death and lead to the treatment of all glaucoma patients.
Tension and compression tuned Bragg grating filter (2002)

A fiber Bragg grating tunable filter based on traction and compression has been realized using two piezoelectric actuators. A linear timing range of 28 nm was obtained.
Power allocation and spectrum sharing in wireless networks: an implementation theory approach (2013)

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CD40 activation of carcinoma cells increases expression of adhesion and major histocompatibility molecules but fails to induce either CD80/CD86 expression or T cell alloreactivity (2001)

A major obstacle for the development of cancer immunotherapy is the poor capacity of most tumor cells to present antigen. It has previously been shown that ligation of CD40 on the surface of malignant B cells results in the induction of efficient antigen presentation primarily because of upregulated expression of MHC, costimulatory, and adhesion molecules. Ongoing clinical trials are testing the impact of CD40 ligation as immunotherapy for B cell malignancies. Because CD40 is also widely expressed in carcinomas, we studied whether CD40 activation of these cells using soluble recombinant trimeric human CD40 ligand (srhCD40L) can also induce T cell responses. Here, we show that carcinoma cells upregulate expression of CD54 and MHC molecules following in vitro exposure to srhCD40L but do not upregulate CD80 or CD86. CD40-activated carcinoma cells failed to trigger mixed lymphocyte reactions, in sharp contrast to CD40-activated lymphoma cells for which CD40 activation, as expected, resulted in increased expression of MHC, adhesion, and costimulatory molecules, and generated brisk allogeneic lymphocyte reactions. Retroviral-mediated expression of CD80 in carcinoma cells, with or without CD40 activation, triggered mixed lymphocyte reactions, provided cells were treated with IFN-gamma. Thus, the cell surface phenotype induced on carcinoma cells following CD40 activation is not fully capable of inducing T cell proliferation; however, these results support ongoing efforts to exploit costimulation in clinical efforts aimed at increasing carcinoma immunogenicity.
Investigation of proton dynamics and the proton transport pathway in choline dihydrogen phosphate using solid-state NMR (2010)

Choline dihydrogen phosphate has previously been shown to be a good ionic conductor as well as an excellent host for acid doping, leading to high proton conductivities required for e.g., electrochemical devices including proton membrane fuel cells and sensors. A combination of variable-temperature (1)H solid-state NMR and 2D NMR pulse sequences, including (31)P and (13)C CODEX and (1)H BaBa, show that the proton conduction mechanism primarily involves assisted transport via a restricted three-site motion of the phosphate unit around the P-O bond that is hydrogen bonded to the choline and exchange of protons between these anions. In other words, proton transport at ambient temperatures appears to occur most favorably along the crystallographic b axis, from phosphate dimer to dimer. At elevated temperatures exchange between the protons of the hydroxyl group on the choline cation and the hydrogen-bonded dihydrogen phosphate groups also contributes to the structural diffusion of the protons in this solid state conductor.
Engineering the Provitamin A (β-Carotene) Biosynthetic Pathway into (Carotenoid-Free) Rice Endosperm (2000)

Rice (Oryza sativa), a major staple food, is usually milled to remove the oil-rich aleurone layer that turns rancid upon storage, especially in tropical areas. The remaining edible part of rice grains, the endosperm, lacks several essential nutrients, such as provitamin A. Thus, predominant rice consumption promotes vitamin A deficiency, a serious public health problem in at least 26 countries, including highly populated areas of Asia, Africa, and Latin America. Recombinant DNA technology was used to improve its nutritional value in this respect. A combination of transgenes enabled biosynthesis of provitamin A in the endosperm.
Erroneous identification of APOBEC3-edited chromosomal DNA in cancer genomics (2014)

Differential DNA denaturation PCR cannot be used to identify fixed C->T transitions in cancer genomes. Presently, the overall mutation frequency is ∼10(4)-10(5) base substitutions per cancer genome, or 0.003-0.03 kb(-1). By contrast, the 3DPCR error rate is of the order of 4-20 kb(-1) owing to constant selection for AT DNA and PCR-mediated recombination. Accordingly, sequences recovered by 3DPCR harbouring mixed C->T and G->A mutations associated with the 5'GpC represent artefacts.
Image stabilization algorithms for video-surveillance applications (2002)

An image stabilization algorithm is presented that is specifically oriented toward video-surveillance applications. The proposed approach is based on a novel motion-compensation method that is an adaptation of a well-known image-stabilization algorithm for visualization in video-surveillance applications. In particular, the illustrated methods take into account the specificity of typical video-surveillance applications, where objects moving in a scene often cover a large part of an image thus causing the failure of classic image-stabilization techniques. Evaluation methods for image stabilization algorithms are discussed.
GlycoMine: a machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome (2015)

Supplementary data are available at Bioinformatics online.
Structural interpretation of the amino acid sequence of a second domain from the Artemia covalent polymer globin. (1990)

Artemia has a complex extracellular hemoglobin of Mr 260,000 comprising two globin chains (Mr 130,000) each of which is a polymer of eight covalently linked domains of Mr 16,000. The primary structure of this polymeric globin was studied to understand how globin folded domains are ordered within a globin chain and, in turn, how the latter associate into a functional hemoglobin molecule. Here we report the amino acid sequence of a second domain, E7 (Mr 16,081, excluding the heme), and interpretations of sequence data by computer-assisted alignment and modeling. This clearly shows that, as with domain E1 (Moens, L., Van Hauwaert, M.-L., De Smet, K., Geelen, D., Verpooten, G., Van Beeumen, J., Wodak, S., Alard, P., & Trotman, C. (1988) J. Biol. Chem. 263, 4679-4685), domain E7 is compatible with a globin folded structure of the beta-type chain. Several specific differences of domains E7 and E1 from the classic globins are identified. They possibly can be interpreted in terms of specific requirements for a double octameric functional molecule.
Hybridization of antisense reagents to RNA. (2000)

Despite the simplicity of the concept, almost every step in an antisense experiment poses difficulties. Finding a site that is accessible to intermolecular hybridization with complementary nucleic acids is a major problem and determines the success or failure of an antisense experiment. A major determinant of accessibility appears to be the intramolecular folding in mRNAs that renders much of the molecule inaccessible. However, owing to our poor understanding of RNA folding and the mechanisms of heteroduplex formation, theoretical methods have limited use in finding accessible sites. Such methods are unable to address two major considerations when designing an antisense reagent, i.e., which is the most accessible sequence in the target and what length of the reagent works best in terms of activity and specificity. Empirical approaches appear more successful. Of notable interest, and reviewed here, are 'global' methods based on DNA arrays and on mapping of transcripts with RNase H.
Isolation and Purification of Medium Chain Length Poly(3-hydroxyalkanoates) (mcl-PHA) for Medical Applications Using Nonchlorinated Solvents (2010)

A novel process was developed to isolate poly([R]-3-hydroxyoctanoate-co-3-hydroxyhexanoate) (PHO) and poly([R]-3-hydroxy-ω-undecenoate-co-3-hydroxy-ω-nonenoate-co-3-hydroxy-ω-heptenoate) (PHUE) from Pseudomonas putida species. Methyl tert-butyl ether (MTBE), ethyl acetate, acetone, and methylene chloride efficiently extracted PHO from freeze-dried biomass. The ratio of solvent to biomass was 15:1 (vol/wt). The nonchlorinated solvents required 18 h of extraction to achieve methylene chloride's yield of 15 wt % within 60 min. In the case of PHUE, the yield was 15-17 wt % after 60 min of extraction at room temperature, independently of the solvent used. MTBE performed best in life cycle assessment (LCA) if contamination of the environment is avoided. Filtration of the extract containing 8 wt % of raw polyhydroxyalkanoate (PHA) through activated charcoal revealed colorless polymers with less than one endotoxin unit/g. The ratio (v/v) of the solution to activated charcoal was 2:1. The loss (impurities and polymers) amounted up to 50 wt %.