gebhart/patrepeval huggingface dataset:
Binding and Uptake of Cationic Lipid: pDNA Complexes by Polarized Airway Epithelial Cells (1999)

To better understand the barriers associated with cationic lipid-mediated gene transfer to polarized epithelial cells, Fischer rat thyroid (FRT) cells and polarized normal human bronchial epithelial (NHBE) cells grown on filter supports at an air-liquid interface were used to study the binding and uptake of cationic lipid:plasmid DNA (pDNA) complexes. The efficiencies of binding and uptake of cationic lipid:pDNA complexes by these cell systems were monitored using fluorescence microscopy of fluorescently tagged lipid or pDNA probes. Fluorescent probe bound to the cell surface was differentiated from internalized probe by adding trypan blue, which quenched the fluorescence of bound but not internalized probes. For proliferating cells, binding and internalization of the cationic lipid:pDNA complexes were determined to be efficient. In contrast, little binding or internalization of the complexes was observed using polarized epithelial cells. However, after aspirating a small area of cells from the filter support, virtually all of the cells adjoining this newly formed edge bound and internalized the cationic lipid:pDNA complexes. To determine if their uptake in edge cells was related to the ability of the complexes to access the basolateral membranes of these cells, the binding and uptake of complexes was monitored in polarized NHBE cells that had been pretreated with EGTA or Ca2+-free media, strategies known to disrupt tight junctions. Cells treated in this manner bound and internalized cationic lipid:pDNA complexes efficiently and also expressed significant levels of transgene product. Control cells with intact tight junctions neither bound complexes nor expressed significant transgene product. These data confirm and extend earlier observations that the polarized apical membranes of airway epithelial cells are resistant to transfection by lipid:pDNA complexes. Further, in contrast to previous studies that have shown the entry step of complexes is not an important barrier for COS and HeLa cells, binding and entry of complexes in polarized NHBE cells appear to be rate limiting. These findings suggest that strategies designed to open the tight junctions of polarized epithelial cells may improve gene delivery to these cells for diseases such as cystic fibrosis (CF).
The Acharistum in a manuscript from the library of Nicholas of Cues (2007)

Collecting mediaeval manuscripts is not what one might call a cardinal sin, unless the collector himself happens to be a cardinal. The cardinal in question would have been one of my closer neighbours, had I lived in the early 15th century. Born in 1401, Nicolaus Cusanus would also have been a close neighbour of Hildegard of Bingen, had she been born three hundred years later. The Cusanus part in Nicholas' name tells us where he came from, the village of Cues (now part of Bernkastel-Kues) on the Moselle river, praised by Ausonius in the 4th century in a Latin poem.
A Porphyromonas gingivalis haloacid dehalogenase family phosphatase interacts with human phosphoproteins and is important for invasion (2006)

Haloacid dehalogenase (HAD) family phosphatases are widespread in prokaryotes and are generally involved in metabolic processes. Porphyromonas gingivalis, an invasive periodontal pathogen, secretes the HAD family phosphoserine phosphatase SerB653 when in contact with gingival epithelial cells. Here we characterize the structure and enzymatic activity of SerB653 and show that a SerB653 allelic replacement mutant of P. gingivalis is deficient in internalization and persistence in gingival epithelial cells. In contrast, mutation of a second HAD family serine phosphatase of P. gingivalis (SerB1170), or of a serine transporter, did not affect invasion. A pull-down assay identified GAPDH and heat-shock protein 90 as potential substrates for SerB653. Furthermore, exogenous phosphatase regulated microtubule dynamics in host cells. These data indicate that P. gingivalis has adapted a formerly metabolic enzyme to facilitate entry into host cells by modulating host cytoskeletal architecture. Our findings define a virulence-related role of a HAD family phosphatase and reveal an invasin of an important periodontal pathogen.
Expression of a fibrinogen fusion peptide in Escherichia coli: a model thrombin substrate for structure/function analysis (1989)

The initial event in fibrin clot formation is the thrombin-catalyzed cleavage of the A alpha chain of human fibrinogen. Most of the information required for thrombin recognition and cleavage of the A alpha chain lies in the amino terminal 51 residue CNBr fragment. By selective modification of residues in this region, we probed the features that participate in thrombin interactions. We constructed a vector which expressed a tripartite protein (tribrid) consisting of amino acids 1 to 50 of the A alpha chain followed by 60 amino acids of chicken collagen and the beta-galactosidase protein from Escherichia coli. Cell lysates run on NaDodSO4-polyacrylamide gels contained the predicted band of molecular weight (mol wt) 125,000. The tribrid reacted with a monoclonal antibody, Mab-Y18, which recognizes the amino terminus of the A alpha chain. When cell lysates were incubated with thrombin, FPA was released. By including one heterogeneous oligonucleotide in the construction, we generated plasmids that encoded three specific amino acid substitutions. Surprisingly, changing Gly14 to Val did not alter thrombin cleavage, although recognition by Mab-Y18 was lost. Substitution of lie for Arg23 did not alter either thrombin cleavage or monoclonal recognition. Substitution of Leu for Arg 16 altered thrombin cleavage; unexpectedly, recognition by Mab-Y18 was not changed.
Generation of cytotoxic T cell responses to an HLA-A24 restricted epitope peptide derived from wild-type p53 (2001)

Mutations in the p53 gene are the most common genetic alterations found in human tumours, and these mutations result in high levels of p53 protein in the tumour cells. Since the expression levels of wild-type p53 in nonmalignant tissue are usually much lower in contrast, the p53 protein is an attractive target for cancer immunotherapy. We tested p53 encoded HLA-A24 binding peptides for their capacity to elicit anti-tumour cytotoxic T lymphocytes (CTL) in vitro. These peptides were in murine p53-derived cytotoxic peptides, which were being presented to CTL by H-2K(d)and H-2K(b)molecules, because the HLA-A24 peptide binding motifs were similar to the H-2K(d)and H-2K(b). For CTL induction, we used CD8(+)T lymphocytes from the peripheral blood mononuclear cells (PBMC) of healthy donors and the peptides from pulsed dendritic cells as antigen-presenting cells. We identified the peptide, p53-161 (AIYKQSQHM), which was capable of eliciting CTL lines that lysed tumour cells expressing HLA-A24 and p53. The effectors lysed C1RA24 cells (p53(+), HLA-A*2402 transfectant), but not their parental cell lines C1R (p53(+), HLA-A,B null cell). These results strongly indicate that the CTL exerts cytotoxic activity in HLA-A24's restricted manner. The identification of this novel p53 epitope for CTL offers the possibility to design and develop specific immunotherapeutic approaches for treating tumours with p53 mutation in HLA-A24-positive patients.
Propylthiouracil-induced chemical hypothyroidism with high-dose tamoxifen prolongs survival in recurrent high grade glioma: a phase I/II study. (2003)

Patients treated for recurrent high-grade gliomas with high-dose tamoxifen had significantly longer survival when chemical hypothyroidism was induced with propylthiouracil.
Femtosecond multiple-pulse impulsive stimulated Raman scattering spectroscopy (1991)

Optical control of elementary molecular motion through impulsive stimulated Raman scattering is enhanced by means of timed sequences of femtosecond pulses that are produced by pulse-shaping techniques. In particular, terahertz-rate trains of femtosecond pulses are used for repetitive impulsive excitation of individual phonon modes in an α-perylene molecular crystal. When the pulse repetition rate is matched to the desired phonon frequency, mode-selective vibrational amplification is achieved. A comparison of data acquired with the transient-grating and the pump–probe experimental geometries reveals the timing dynamics of the induced phonon oscillations with respect to the driving femtosecond pulse sequence.
Concentration and Behavior of Carbon in Semiconductor Silicon (1970)

The concentration of carbon in semiconductor silicon and the behavior of carbon in the fusion and crystallization of silicon have been studied by the use of charged particle activation analysis. The solubility of carbon in solid silicon has been found to be or slightly less at the melting point, and the equilibrium distribution coefficient of carbon between solid and liquid silicon has been determined to be . Carbon content over the above solubility value has seldom been observed in silicon single crystals produced by modern industrial techniques. The content appears to depend more on the growth conditions of the single crystal than on the chemical purification method. The phase diagram of the C‐Si system in the extremely low carbon concentration range is given, together with a discussion of the kinematics of the carbon behavior in zone melting. Also, a new technique for studying the evaporation of carbon from the silicon melt is shown.
Large-scale deep unsupervised learning using graphics processors (2009)

The promise of unsupervised learning methods lies in their potential to use vast amounts of unlabeled data to learn complex, highly nonlinear models with millions of free parameters. We consider two well-known unsupervised learning models, deep belief networks (DBNs) and sparse coding, that have recently been applied to a flurry of machine learning applications (Hinton & Salakhutdinov, 2006; Raina et al., 2007). Unfortunately, current learning algorithms for both models are too slow for large-scale applications, forcing researchers to focus on smaller-scale models, or to use fewer training examples.
Impact of Influenza Vaccination on Seasonal Mortality in the US Elderly Population (2005)

We attribute the decline in influenza-related mortality among people aged 65 to 74 years in the decade after the 1968 pandemic to the acquisition of immunity to the emerging A(H3N2) virus. We could not correlate increasing vaccination coverage after 1980 with declining mortality rates in any age group. Because fewer than 10% of all winter deaths were attributable to influenza in any season, we conclude that observational studies substantially overestimate vaccination benefit.
Unraveling structural and compositional information in 3D FinFET electronic devices (2019)

Non-planar Fin Field Effect Transistors (FinFET) are already present in modern devices. The evolution from the well-established 2D planar technology to the design of 3D nanostructures rose new fabrication processes, but a technique capable of full characterization, particularly their dopant distribution, in a representative (high statistics) way is still lacking. Here we propose a methodology based on Medium Energy Ion Scattering (MEIS) to address this query, allowing structural and compositional quantification of advanced 3D FinFET devices with nanometer spatial resolution. When ions are backscattered, their energy losses unfold the chemistry of the different 3D compounds present in the structure. The FinFET periodicity generates oscillatory features as a function of backscattered ion energy and, in fact, these features allow a complete description of the device dimensions. Additionally, each measurement is performed over more than thousand structures, being highly representative in a statistical meaning. Finally, independent measurements using electron microscopy corroborate the proposed methodology.
Deep learning based image super-resolution with coupled backpropagation (2016)

Recently deep learning methods have been applied to image super-resolution (SR). Typically, these approaches involve training a single convolutional neural network that is trained to perform resolution enhancement. We propose a new low-complexity but effective algorithm called Superresolution with Coupled Backpropagation (SR-CBP) which builds two Coupled Auto-encoder Networks (CAN), resp. the high-resolution (HR) and low-resolution (LR) networks, that capture the features of both high and low resolution images. The two networks in CAN have the ability to self-reconstruct its own input. Specifically, SR-CBP allows joint training of the LR and HR networks to have middle layer representations that agree for a pair of images (high-resolution image and its corresponding low-resolution version). For an LR input image, its middle layer representation obtained via the trained LR network can be fed into the HR network to generate the SR result. Preliminary experiments show that SR-CBP can produce better results than state of the art single image superresolution methods based on sparse representations. The memory and storage requirements of CAN are lesser than existing deep learning based SR methods.
Cross-reactions and specificities of monoclonal antibodies against myelin basic protein and against the synthetic copolymer 1. (1991)

Antibody cross-reactivity is here demonstrated between basic protein (BP), the encephalitogenic molecule of myelin, and copolymer 1 (Cop 1), the synthetic amino acid copolymer, which has a suppressive effect on experimental allergic encephalomyelitis and is effective in reducing the number of relapses in exacerbating-remitting multiple sclerosis. This cross-reactivity is conclusively established using mouse monoclonal antibodies (mAbs). About a third of anti-rat BP mAbs and most of anti-mouse BP mAbs cross-reacted with Cop 1. This cross-reactivity could be demonstrated with anti-BP mAbs of different specificities. In addition, several anti-Cop 1 hybridomas cross-reacted with BP. This cross-reactivity was verified in several assay systems, including competitive inhibition experiments. Moreover, some anti-BP mAbs and anti-Cop 1 mAbs reacted in a heteroclitic manner and favored the cross-reactive antigen over the immunogen. In contrast to the mAbs, no cross-reactivity could be demonstrated with the antisera of immunized mice. This observation may reflect the different B-cell populations expressed in the mAb response as compared to the polyclonal response. Thus, the use of mAbs has uncovered specificities that are not evident in antisera and has revealed pronounced cross-reactivity between BP and Cop 1 at the B-cell level. These results further establish the immunological interrelationships between Cop 1 and BP, demonstrated earlier at the T-cell level.
Reliability and validity of a new global dyskinesia rating scale in the MPTP‐lesioned non‐human primate (2001)

Behavioral rating scales for dyskinesia in the non-human primate are frequently used to assess the efficacy of new treatments and to provide a clinical correlative with neurochemical and neuropathological changes. Although a large variety of different scales have been used in non-human primate studies, there is no single standardized scale, and none have been evaluated for reliability and validity. We are reporting a new global non-human primate dyskinesia rating scale (GPDRS) for the squirrel monkey, developed in the context of an independent study of dyskinesia. In this report we demonstrate the reliability and validity of this scale. The GPDRS is a single-item scale with well-defined points and brevity allowing for rapid and easy application for assessing the overall degree of dyskinesia. In this study, seven MPTP-lesioned and four non-lesioned (control) non-human primates were videotaped following treatment with either levodopa or water. To test inter- and intra-rater reliability, three examiners rated the videotape independently at two different time points and these assessments were compared. The validity of the scale was tested in two phases. First, examiners rated the videotape using the GPDRS and the Abnormal Involuntary Movement Scale (AIMS), a scale commonly used to rate dyskinesia in the non-human primate, and the ratings from each scale were compared. Second, validity was tested in the context of an independent dyskinesia study, in which the scale was used to distinguish between two treatment groups. The GPDRS was shown to have high inter- and intra-rater reliability and to be valid for the assessment of dyskinesia in the squirrel monkey. In this report we also demonstrate the inter- and intra-rater reliability of the AIMS.
Molecular and Genetic Basis of Prion Diseases (1998)

Prions cause a group of human and animal neurodegenerative diseases that are now classified together because their etiology and pathogenesis involve modification of the prion protein (PrP). Prion diseases are manifest as infectious, genetic, and sporadic disorders (Table 102-1). These diseases can be transmitted among mammals by the infectious particle designated "prion." Despite intensive searches over the past three decades, no nucleic acid has been found within prions; yet, a modified isoform of the host-encoded PrP designated PrPSc is essential for infectivity. In fact, considerable experimental data argue that prions are composed exclusively of PrPSc. Earlier terms used to describe the prion diseases include transmissible encephalopathies, spongiform encephalopathies, and slow virus diseases.
Direct drawing on 3D shapes with automated camera control (2014)

We present ACCD, an interaction technique that allows direct drawing of long curves on 3D shapes with a tablet display over both multiple depth layers and multiple viewpoints. ACCD reduces the number of explicit viewpoint manipulations by combining self-occlusion management and automated camera control. As such it enables drawing on occluded faces but also around a 3D shape while keeping a constant drawing precision. Our experimental results indicates the efficacy of ACCD over conventional techniques.
Detection of ras gene mutations in peripheral blood of carcinoma patients using CD45 immunomagnetic separation and nested mutant allele specific amplification. (1998)

We developed a sensitive technique of detecting circulating tumor cells in carcinoma patients, using CD45 immunomagnetic separation to isolate epithelial cells in blood samples and specific polymerase chain reaction analysis to identify point mutations of the K-ras gene. The method is based on the fact that the peripheral blood mononuclear cells (PBMC) that express CD45 antigen are trapped with anti-CD45 conjugated supramagnetic microbeads while the carcinoma cells that do not express CD45 antigen are not trapped and pass through the magnetic fields. This method concentrated the number of carcinoma cells 3.3 times. After this separation, the modified method of mutant allele specific amplification was applied and this method was able to ten control carcinoma cells in a background of 107 PBMC. A preliminary clinical study demonstrated that six cases of end-stage carcinoma with K-ras mutations in the primary tumor showed the same mutations in the peripheral blood samples, while two cases without K-ras mutation in the primary tumor and 10 healthy volunteers showed no mutation in the peripheral blood samples. The results suggest that this method may be very useful to detect circulating carcinoma cells in the patient whose primary tumor shows K-ras mutations.
Topical application of 1-methylnicotinamide in the treatment of rosacea: a pilot study (2005)

Rosacea is a chronic facial dermatosis with a progressive course, which is characterized by the presence of erythema, papules, pustules, telangiectasias and sebaceous gland hyperplasia. However, the aetiology is still unknown; genetic predisposition, gastrointestinal disorders (Helicobacter pylori), infestations with Demodex folliculorum and environmental stimuli are considered to be involved in the inflammatory process. A metabolite of nicotinamide, 1-methylnicotinamide (MNA(+)), has anti-inflammatory properties, and this is the first study to test the effectiveness of this agent in treating rosacea. In total, 34 patients with rosacea were treated with a gel containing 0.25% MNA(+) as a chloride salt, twice daily for 4 weeks, after which improvement was observed in 26/34 cases. The improvement was good in 9/34 and moderate in 17/34, but no clinical effect was noted in seven subjects. In only one case was skin irritation given as the reason for treatment withdrawal. These results indicate that MNA(+) might be a useful agent for treating rosacea.
Butyrate inhibits inflammatory responses through NFκB inhibition: implications for Crohn's disease (2000)

Butyrate decreases proinflammatory cytokine expression via inhibition of NFkappaB activation and IkappaBalpha degradation. These anti-inflammatory properties provide a rationale for assessing butyrate in the treatment of CD.
Exploiting hardware heterogeneity within the same instance type of Amazon EC2 (2012)

Cloud computing providers might start with nearhomogeneous hardware environment. Over time, the homogeneous environment will most likely evolve into heterogeneous one because of possible upgrades and replacement of outdated hardware. In turn, the hardware heterogeneity will result into performance variation. In this paper, we look into the hardware heterogeneity and the corresponding performance variation within the same instance type of Amazon Elastic Compute Cloud (Amazon EC2). Standard large instance is selected as the example. We find out that there exist three different subtypes of hardware configuration in the standard large instance. Through a set of detailed micro-benchmark and application-level benchmark measurements, we observe that the performance variation within the same sub-type of instance is relatively small, whilst the variation between different sub-types can be up to 60%. By selecting better-performing instances to complete the same task, end-users of Amazon EC2 platform can achieve up to 30 % cost saving. 1
The CXCR5 Chemokine Receptor Is Expressed by Carcinoma Cells and Promotes Growth of Colon Carcinoma in the Liver (2006)

The chemokine receptor CXCR5 is expressed by B cells and certain T cells and controls their migration into and within lymph nodes. Its ligand BCA-1/CXCL13 is present in lymph nodes and spleen and also in the liver. Surprisingly, we detected CXCR5 in several mouse and human carcinoma cell lines. CXCR5 was particularly prominent in pancreatic carcinoma cell lines and was also detected by immunohistochemistry in 7 of 18 human pancreatic carcinoma tissues. Expression in CT26 colon carcinoma was low in vitro, up-regulated in vivo, and rapidly lost when cells were explanted in vitro. CXCL13 strongly promoted proliferation of CXCR5-transfected CT26 cells in vitro. In the liver, after intrasplenic injection, these CXCR5 transfectants initially grew faster than controls, but the growth rate of control tumors accelerated later to become similar to the transfectants, likely due to the up-regulation of CXCR5. Inhibition of CXCR5 function, by trapping CXCR5 in the endoplasmic reticulum using a CXCL13-KDEL "intrakine," had no effect on initial growth of liver foci but later caused a prolonged growth arrest. In contrast, s.c. and lung tumors of CXCR5- and intrakine-transfected cells grew at similar rates as controls. We conclude that expression of CXCR5 on tumor cells promotes the growth of tumor cells in the liver and, at least for CT26 cells, seems to be required for outgrowth to large liver tumors. Given the limited expression on normal cells, CXCR5 may constitute an attractive target for therapy, particularly for pancreatic carcinoma.