gebhart/patrepeval huggingface dataset:
A System for Small-Molecule Control of Conditionally Replication-Competent Adenoviral Vectors (2002)

Replication-competent adenoviral vectors are potentially far more efficient than replication-defective vectors. However, for reasons of safety, there is a need to restrict viral replication both spatially, by limiting replication to certain cell types, and temporally. To control replication temporally, we have developed a system, based on the small-molecule dimerizer rapamycin, for regulating the replication of adenoviral vectors. In this system, one adenoviral vector, AdC4, expresses transcription factors whose activity is regulated by the non-immunosuppressive rapamycin analog AP21967. A second vector, Ad(Z12-I-E1aE1b19k), contains E1 genes placed downstream of binding sites for the regulated transcription factor. Co-infection of several cell lines by the vector pair leads to dimerizer-dependent E1 expression and an increase in viral replication, as shown by Southern blots and replication assays. Furthermore, expression of a reporter gene from a replication-defective vector, Ad-GM-CSF, can be augmented by up to 18-fold by co-infection with the pair of conditionally replicating vectors in the presence of dimerizer. Similar results are obtained when the vectors are directly injected into subcutaneous HT1080 xenograft tumors in nude mice. We believe that vectors based on this principle will be a useful additional tool to enhance efficiency and safety of gene delivery for anti-cancer therapy.
Idiopathic pulmonary fibrosis (2008)

Idiopathic pulmonary fibrosis (IPF) is a non-neoplastic pulmonary disease that is characterized by the formation of scar tissue within the lungs in the absence of any known provocation. IPF is a rare disease which affects approximately 5 million persons worldwide. The prevalence is estimated to be slightly greater in men (20.2/100,000) than in women (13.2/100,000). The mean age at presentation is 66 years. IPF initially manifests with symptoms of exercise-induced breathless and dry coughing. Auscultation of the lungs reveals early inspiratory crackles, predominantly located in the lower posterior lung zones upon physical exam. Clubbing is found in approximately 50% of IPF patients. Cor pulmonale develops in association with end-stage disease. In that case, classic signs of right heart failure may be present. Etiology remains incompletely understood. Some environmental factors may be associated with IPF (cigarette smoking, exposure to silica and livestock). IPF is recognized on high-resolution computed tomography by peripheral, subpleural lower lobe reticular opacities in association with subpleural honeycomb changes. IPF is associated with a pathological lesion known as usual interstitial pneumonia (UIP). The UIP pattern consists of normal lung alternating with patches of dense fibrosis, taking the form of collagen sheets. The diagnosis of IPF requires correlation of the clinical setting with radiographic images and a lung biopsy. In the absence of lung biopsy, the diagnosis of IPF can be made by defined clinical criteria that were published in guidelines endorsed by several professional societies. Differential diagnosis includes other idiopathic interstitial pneumonia, connective tissue diseases (systemic sclerosis, polymyositis, rheumatoid arthritis), forme fruste of autoimmune disorders, chronic hypersensitivity pneumonitis and other environmental (sometimes occupational) exposures. IPF is typically progressive and leads to significant disability. The median survival is 2 to 5 years from the time of diagnosis. Medical therapy is ineffective in the treatment of IPF. New molecular therapeutic targets have been identified and several clinical trials are investigating the efficacy of novel medication. Meanwhile, pulmonary transplantation remains a viable option for patients with IPF. It is expected that, during the next decade, considerable progress will be made toward the understanding and treatment of this devastating illness.
Blockwise mechanical synthesis of oligonucleotides by the phosphoramidite method. (1987)

For use in automated synthesis of oligodeoxyribonucleotides, a dimer containing the triesterified internucleotide linkage and the 3 '-phosphoramidite has been prepared. 5 '-O-Dimethoxytritylthymidylyl- (3 '-5') - (o-chlorophenyl) -thymidine was converted to the 3 '- (methyl)N , N-diisopropylphosphoramidite, which has been used as a condensing unit for the synthesis of pentadecathymidylate on controlled pore glass by a deoxyribonucleic acid (DNA) synthesizer.
Bevacizumab and ovarian cancer (2012)

Bevacizumab is a recombinant humanized monoclonal IgG1 antibody that targets vascular endothelial growth factor-A, and is indicated in the treatment of various tumors (colon, lung, renal, and glioblastoma). It has been recently approved for the treatment of ovarian cancer in various countries. This review summarizes the activity and toxicity of bevacizumab in the treatment of ovarian cancer, both as single-agent drug and in combination with cytotoxic chemotherapy. As a single-agent drug, it has shown response rates of 16-21% in the treatment of recurrent ovarian cancer. Two phase III randomized trials have been published evaluating the addition of bevacizumab to standard chemotherapy as front-line treatment of advanced ovarian cancer. In addition, trials evaluating the combination with chemotherapy in recurrent ovarian cancer (platinum-sensitive and platinum-resistant disease) have also been reported. All these trials showed a statistically significant improvement in progression-free survival although no improvement in overall survival has been reported. The main adverse event is hypertension. Other serious, but uncommon adverse events include gastrointestinal perforation as well as renal and central nervous system toxicity.
Durable silver coating for Kepler Space Telescope primary mirror (2008)

A durable silver coating was developed and applied to the Kepler Space Telescope primary mirror. The coating was manufactured by an ion-assisted evaporation process and coating uniformity was better than 30-nm PTV over the 1.4-m mirror aperture. The protection scheme for silver was devised and patented twelve years ago by Lawrence Livermore National Laboratory (LLNL) in the United States. An interference coating was added to the basic protected silver design, to enhance the reflectance from 400-nm to the near infrared.
Simultaneous colorimetric detection of improvised explosive compounds using microfluidic paper-based analytical devices (μPADs) (2014)

In this paper the development of microfluidic paper-based analytical devices (μPADs) is described for the rapid, on-site detection of improvised explosives.
Three-dimensional porous V2O5 cathode with ultra high rate capability (2011)

Three-dimensional (3D) porous vanadium pentoxide (V2O5) thin films were synthesized by electrostatic spray deposition followed by annealing at 350 °C in air. The interconnected pore networks facilitate the kinetics of lithium-ion diffusion and help the porous V2O5 with stable capacity, high energy efficiency and excellent rate capability as a cathode material for lithium batteries.
Multi-Element Fiber Technology for Space-Division Multiplexing Applications (2014)

A novel technological approach to space division multiplexing (SDM) based on the use of multiple individual fibers embedded in a common polymer coating material is presented, which is referred to as Multi-Element Fiber (MEF). The approach ensures ultralow crosstalk between spatial channels and allows for cost-effective ways of realizing multi-spatial channel amplification and signal multiplexing/demultiplexing. Both the fabrication and characterization of a passive 3-element MEF for data transmission, and an active 5-element erbium/ytterbium doped MEF for cladding-pumped optical amplification that uses one of the elements as an integrated pump delivery fiber is reported. Finally, both components were combined to emulate an optical fiber network comprising SDM transmission lines and amplifiers, and illustrate the compatibility of the approach with existing installed single-mode WDM fiber systems.
Temporary gastric neuromodulation for intractable nausea and vomiting (2011)

GNM improved upper gastrointestinal symptoms, quality of life and nutritional status in patients with intractable nausea and vomiting. GNM merits further investigation.
Intravesical ALT-803 and BCG Treatment Reduces Tumor Burden in a Carcinogen Induced Bladder Cancer Rat Model; a Role for Cytokine Production and NK Cell Expansion (2014)

Intravesical Bacillus Calmette-Guérin (BCG) has been shown to induce a specific immunologic response (i.e., activation of IL-2 and effector T-cells), while preclinical studies using ALT-803 (mutated IL-15 analogue combined with IL-15Rα-Fc fusion) have shown promising results by prolonging the agent's half-life and stimulating CD8+ T-cells. Based on these results, we hypothesized that the intravesical administration of ALT-803 along with BCG will generate an immunologic response leading to significant bladder tumor burden reduction. Using a well-established carcinogen induced rat non-muscle invasive bladder cancer (NMIBC) model, we studied the effects of intravesical ALT-803 with and without BCG. Rat tissues were evaluated to document treatment response. Intravesical ALT-803 was safe and well tolerated alone and in combination with BCG. As a single treatment agent, ALT-803 reduced tumor burden by 35% compared to control whereas BCG alone only reduced tumor burden by 15%. However, the combination of ALT-803 plus BCG reduced tumor burden by 46% compared to control. Immune monitoring suggested that the antitumor response was linked to the production and secretion of IL-1α, IL-1β and RANTES, which in turn, induced the proliferation and activation of NK cells. Lastly, tumoral responses of the combinational treatment were associated with 76% reduction in angiogenesis, which is significantly higher than when assessed with either agent alone. The enhanced therapeutic index seen with this duplet provides justification for the development of this regimen for future clinical trials.
Time series analysis in the time domain and resampling methods for studies of functional magnetic resonance brain imaging (1997)

Although functional magnetic resonance imaging (fMRI) methods yield rich temporal and spatial data for even a single subject, universally accepted data analysis techniques have not been developed that use all the potential information from fMRI of the brain. Specifically, temporal correlations and confounds are a problem in assessing change within pixels. Spatial correlations across pixels are a problem in determining regions of activation and in correcting for multiple significance tests. We propose methods that address these issues in the analysis of task-related changes in mean signal intensity for individual subjects. Our approach to temporally based problems within pixels is to employ a model based on autoregressive-moving average (ARMA or "Box-Jenkins") time series methods, which we call CARMA (Contrasts and ARMA). To adjust for performing multiple significance tests across pixels, taking into account between-pixel correlations, we propose adjustment of P values with "resampling methods." Our objective is to produce two- or three-dimensional brain maps that provide, at each pixel in the map, an estimated P value with absolute meaning. That is, each P value approximates the probability of having obtained by chance the observed signal effect at that pixel, given that the null hypothesis is true. Simulated and real data examples are provided.
Proton NMR study of the state of water in fibrin gels, plasma, and blood clots (1990)

A proton NMR relaxation and pulsed field gradient self-diffusion study of water in fibrin gels, plasma, and blood clots has been performed with special emphasis on the effect of the sol-gel and shrinkage transitions. Deuteron NMR in fibrin gels was also studied to supplement the proton data. It is shown that a measurement of the water proton or deuteron T1/T2 ratio allows for a determination of the bound water fraction in all these systems. The change in the T1/T2 ratio at the shrinkage transition further allows for a determination of the surface fractal dimension of the gel if the change in the volume of the gel is known. The self-diffusion coefficient of water in these systems, which determines the transport properties of the gel, is found to be proportional to the free water fraction in both the nonshrunken and shrunken state.
Effects of Laser Radiation on Biological Systems. (1964)

s1 April 1964Effects of Laser Radiation on Biological Systems.Edmund Klein, M.D., Elias Cohen, M.D., Julian Ambrus, M.D., Samuel Fine, M.S.Edmund Klein, M.D.Search for more papers by this author, Elias Cohen, M.D.Search for more papers by this author, Julian Ambrus, M.D.Search for more papers by this author, Samuel Fine, M.S.Search for more papers by this authorAuthor, Article, and Disclosure Informationhttps://doi.org/10.7326/0003-4819-60-4-725_3 SectionsAboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissions ShareFacebookTwitterLinkedInRedditEmail ExcerptStudies on the effects of laser radiation in normal and tumor bearing animals and on isolated biological systems have been carried out. Animals included hamsters, mice, rats, and monkeys. The in vitro systems included viable mammalian cells, unicellular organisms and macromolecular preparations of biological origin. Our studies were carried out at 10,600 Å, 6943 Å and 6328 Å, at energy levels from the millijoule region to more than 500 joules, peak power levels exceeding 100 Mw and pulse repetition frequencies of 1/sec. The qualitative and quantitative aspects of the biological effects varied with the characteristics of the radiation. Effects on... This content is PDF only. To continue reading please click on the PDF icon. Author, Article, and Disclosure InformationAffiliations: PreviousarticleNextarticle Advertisement FiguresReferencesRelatedDetails Metrics 1 April 1964Volume 60, Issue 4Page: 725-726KeywordsCellsHeart rateSystems biology Issue Published: 1 April 1964 PDF downloadLoading ...
Frequency-chirped subwavelength nanoantennas (2012)

Herein we propose, theoretically investigate, and numerically demonstrate the first use to our knowledge of frequency chirping to achieve broadband, efficient subwavelength vertical emission from a dielectric waveguide. We demonstrate this unique and effective approach in the telecom C band in a nanophotonic frequency-chirped dipole antenna. The structure utilizes a plasmonic antenna placed above an Si3N4 waveguide and a ground plane to enhance emission efficiency. Three-dimensional finite-difference time-domain simulations reveal up to 55% vertical emission efficiency, and a bandwidth of 500 nm is possible in a structure less than half a wavelength long. The design methodology and theoretical underpinnings of frequency-chirped nanophotonic antennas coupled to dielectric waveguides are presented.
High-performance nMOSFETs using a novel strained Si/SiGe CMOS architecture (2003)

Performance enhancements of up to 170% in drain current, maximum transconductance, and field-effect mobility are presented for nMOSFETs fabricated with strained-Si channels compared with identically processed bulk Si MOSFETs. A novel layer structure comprising Si/Si/sub 0.7/Ge/sub 0.3/ on an Si/sub 0.85/Ge/sub 0.15/ virtual substrate (VS) offers improved performance advantages and a strain-compensated structure. A high thermal budget process produces devices having excellent on/off-state drain-current characteristics, transconductance, and subthreshold characteristics. The virtual substrate does not require chemical-mechanical polishing and the same performance enhancement is achieved with and without a titanium salicide process.
Enhanced antitumor activity and selectivity of lactoferrin‐derived peptides (2002)

A number of peptide analogs derived from the N-terminal alpha-helical region of bovine lactoferrin (LFB 14-31), were designed in order to investigate how deviating numbers and positions of positively charged residues and numbers of aromatic residues affected their activity against prokaryotic, normal and transformed eukaryotic cells. Most of the LFB derivatives were highly active against both Escherichia coli and Staphylococcus aureus. The peptides were more active against the tumor cell lines MethA, HT-29 and MT-1 than normal eukaryotic cells. The peptides that were most active against the tumor cell lines had all cationic residues concentrated in one sector of the helical structure. These peptides were less selective against the tumor cell lines than against normal fibroblasts. Quantitative structure-activity relationship studies showed that certain structural parameters affected toxicity against the tumor cell lines more than against fibroblasts. Peptides encompassing these parameters were slightly less active against tumor cells, but gained significant selectivity.
A 1.32 TOPS/W Energy Efficient Deep Neural Network Learning Processor with Direct Feedback Alignment based Heterogeneous Core Architecture (2019)

An energy efficient deep neural network (DNN) learning processor is proposed using direct feedback alignment (DFA). The proposed processor achieves 2.2 × faster learning speed compared with the previous learning processors by the pipelined DFA (PDFA). In order to enhance the energy efficiency by 38.7%, the heterogeneous learning core (LC) architecture is optimized with the 11-stage pipeline data-path. Furthermore, direct error propagation core (DEPC) utilizes random number generators (RNG) to remove external memory access (EMA) caused by error propagation (EP) and improve the energy efficiency by 19.9%. The proposed PDFA based learning processor is evaluated on the object tracking (OT) application, and as a result, it shows 34.4 frames-per-second (FPS) throughput with 1.32 TOPS/W energy efficiency.
Aberrant expression of SWI/SNF catalytic subunits BRG1/BRM is associated with tumor development and increased invasiveness in prostate cancers (2006)

We provide the first evidence that aberrant expression of BRG1 and BRM genes is associated with disease development and progression in prostate cancers and increased BRG1 expression may promote tumor growth and invasion.
The human fibroblast and human immune interferon genes and their expression in homologous and heterologous cells (1982)

The genetic information coding for human fibroblast interferon (IFN-beta) has been cloned both as a DNA copy (cDNA) and as a genomic clone. Human IFN-beta is made as a precursor and consists of a signal sequence 21 amino acid residues long followed by the mature protein 166 amino acids long. A single site for glycosylation is present. The human IFN-beta gene does not contain introns. Transfection of monkey cells with a chimeric SV40 derivative containing the human IFN-beta cDNA clone under control of the late SV40 promoter leads to secretion of high levels of IFN-beta. When a genomic clone is used in the same vector, IFN-beta synthesis can be further enhanced up to 30-fold by treatment with poly(rI) . poly(rC); this shows that a cis-active control element is present in the clone. An efficient expression system in Escherichia coli was worked out based on a plasmid containing the promoter PL of bacteriophage lambda, which is regulated by a temperature-sensitive repressor. This promoter is followed by a segment derived from bacteriophage MS2 that contains the ribosome-binding site of the replicase gene. The latter, however, is replaced by the human IFN-beta gene. Upon induction, high levels (about 5 x 10(9) IU 1(-1)) of IFN-beta are synthesized by the bacteria; this corresponds to about 2% of the total bacterial protein. The human immune (type II) interferon (IFN-gamma) gene has similarly been cloned. Partly purified mRNA derived from human spleen cells that had been induced with staphylococcal enterotoxin A was used as starting material. A full-length cDNA clone was sequenced. The total cDNA sequence is about 1150 nucleotides long; it contains a single open reading frame coding for 166 amino acids, the first 20 of which constitute the transmembrane signal. There are two sites for glycosylation. The amino acid sequence is quite different from that of IFN-alpha or IFN-beta, although a few similarities can be noted. The untranslated 3'-terminal region is about 550 nucleotides long. The IFN-gamma gene was expressed in monkey cells, again by using the SV40-derived vector, and the secreted product was characterized as true human IFN-gamma. A genomic clone in the form of a bacteriophage lambda derivative was also obtained. The IFN-gamma gene extends over at least 5 kilobases and contains at least two introns.
Crack-Cocaine Use Accelerates HIV Disease Progression in a Cohort of HIV-Positive Drug Users (2008)

Crack-cocaine use facilitates HIV disease progression by reducing adherence in those on HAART and by accelerating disease progression independently of HAART.
Super resolution video by using classified multi-filter up-sampling algorithm (2011)

H.264/Scalable Video Coding (SVC) is the extension of the H.264/AVC which is developed by the Joint Video Team (JVT) and Moving Picture Experts Group (MPEG). The extension allows multiple resolutions of an image sequence to be contained in a single bit stream. The various resolutions can be achieved by up-sampling a lower image resolution sequence. The up-sampling method employed in H.264/SVC is directly proportional to the video quality. In order to improve the video quality with an effective up-sampler, we propose a classified multi-filter up-sampling algorithm for H.264/SVC in spatial scalability which classifies an image region as edges and non edges. An appropriate filter is then applied to up-sample the image. In the proposed scheme, we applied the Wiener filter for edges and conventional bilinear filter for non edges within the defined window size to preserve the edges in the up-sampled image sequence. The experimental results show that the average PSNR improvement and bit-rate reduction are 0.4 dB and 7%, respectively, which confirm that the performance of the proposed method is better than that of the existing H.264/Scalable Video Coding standard.
Deep belief network based semantic taggers for spoken language understanding (2013)

This paper investigates the use of deep belief networks (DBN) for semantic tagging, a sequence classification task, in spoken language understanding (SLU). We evaluate the performance of the DBN based sequence tagger on the well-studied ATIS task and compare our technique to conditional random fields (CRF), a state-of-the-art classifier for sequence classification. In conjunction with lexical and named entity features, we also use dependency parser based syntactic features and part of speech (POS) tags [1]. Under both noisy conditions (output of automatic speech recognition system) and clean conditions (manual transcriptions), our deep belief network based sequence tagger outperforms the best CRF based system described in [1] by an absolute 2% and 1% F-measure, respectively.Upon carrying out an analysis of cases where CRF and DBN models made different predictions, we observed that when discrete features are projected onto a continuous space during neural network training, the model learns to cluster these features leading to its improved generalization capability, relative to a CRF model, especially in cases where some features are either missing or noisy.