gebhart/patrepeval huggingface dataset:
Selection of a Respiratory Syncytial Virus Fusion Inhibitor Clinical Candidate. 2. Discovery of a Morpholinopropylaminobenzimidazole Derivative (TMC353121) (2008)

A preceding paper (Bonfanti et al. J. Med Chem. 2007, 50, 4572-4584) reported the optimization of the pharmacokinetic profile of substituted benzimidazoles by reducing their tissue retention. However, the modifications that were necessary to achieve this goal also led to a significant drop in anti-RSV activity. This paper describes a molecular modeling study followed by a lead optimization program that led to the recovery of the initial potent antiviral activity and the selection of TMC353121 as a clinical candidate.
Novel Minicircle Vector for Gene Therapy in Murine Myocardial Infarction (2009)

Taken together, this is the first study to our knowledge to demonstrate that MC can significantly improve transfection efficiency, duration of transgene expression, and cardiac contractility. Given the serious drawbacks associated with most viral vectors, we believe this novel nonviral vector can be of great value for cardiac gene therapy protocols.
Effect of an Extract of the Chinese Herbal Remedy <i>Tripterygium Wilfordii</i> Hook F on Human Immune Responsiveness (1991)

Tripterygium wilfordii Hook F (TWH) is a vine-like plant that grows in a wide area of south China. An alcohol extract of this plant known as T2 has been suggested to be effective in the treatment of rheumatoid arthritis (RA). To examine the mechanism by which this herbal remedy might be effective in RA, the capacity of T2 to alter human immune responsiveness in vitro was investigated. Human peripheral blood mononuclear cells were obtained from normal adults and separated into purified populations of monocytes, T cells, and B cells. T2 at 0.1-1 micrograms/ml inhibited antigen- and mitogen-stimulated proliferation of T cells and B cells, interleukin-2 (IL-2) production by T cells, and immunoglobulin production by B cells. T2 did not affect IL-2 receptor expression by T cells, IL-1 production by monocytes, or the capacity of monocytes to present antigen. Inhibition could not be accounted for by nonspecific toxicity. These results support the conclusion that T2 exerts a powerful suppressive effect on human immune responses. This action might account for its therapeutic effectiveness in RA.
Genomic-assisted phylogenetic analysis and marker development for next generation soybean cyst nematode resistance breeding (2015)

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a serious soybean pest. The use of resistant cultivars is an effective approach for preventing yield loss. In this study, 19,652 publicly available soybean accessions that were previously genotyped with the SoySNP50K iSelect BeadChip were used to evaluate the phylogenetic diversity of SCN resistance genes Rhg1 and Rhg4 in an attempt to identify novel sources of resistance. The sequence information of soybean lines was utilized to develop KASPar (KBioscience Competitive Allele-Specific PCR) assays from single nucleotide polymorphisms (SNPs) of Rhg1, Rhg4, and other novel quantitative trait loci (QTL). These markers were used to genotype a diverse set of 95 soybean germplasm lines and three recombinant inbred line (RIL) populations. SNP markers from the Rhg1 gene were able to differentiate copy number variation (CNV), such as resistant-high copy (PI 88788-type), low copy (Peking-type), and susceptible-single copy (Williams 82) numbers. Similarly, markers for the Rhg4 gene were able to detect Peking-type (resistance) genotypes. The phylogenetic information of SCN resistance loci from a large set of soybean accessions and the gene/QTL specific markers that were developed in this study will accelerate SCN resistance breeding programs.
Near-IR imaging microscopy using an acousto-optic tunable filter (AOTF) (1992)

Near-infrared spectroscopy is a sensitive and non-invasive probe for chemical analyses. The integration of spectroscopic and imaging technologies is a potent tool for the study of a wide range of biological materials. Continuously tunable acousto-optic filters operable in the ultraviolet, visible and infrared are now widely available. These computer controlled notch filters provide random wavelength access, wide spectral coverage and moderate spectral resolution. AOTFs potentially have a wide range of spectroscopic applications. We employ AOTF technology for visible/NIR absorption microscopy between 600-2000 nm. The microscope is constructed around an acousto-optic device coupled to an infinity corrected microscope employing either silicon or indium antinomide focal-plane array detectors. In operation, the AOTF is used to spectrally filter a quartz halogen light source. Under computer control the AOTF is swept through a wavelength range and at predetermined intervals images are recorded. Hundreds of frames may be collected, and the spectral image data set can readily comprise many megabytes of data.
Multi-mode pumped amplifier using a newly developed 8-cm long erbium-doped phosphate glass fiber (2002)

A fiber amplifier with a net gain of 43dB at 1535nm and 21dB over the full C-band was demonstrated using a newly developed 8-cm long erbium-doped phosphate fiber excited with a 1 W 975nm multimode laser diode. A theoretical model was developed for multi-mode pumped amplifier using a very short fiber.
Mixed Matrix Membranes from a Microporous Polymer Blend and Nanosized Metal–Organic Frameworks with Exceptional CO<sub>2</sub>/N<sub>2</sub> Separation Performance (2020)

Most examples of mixed-matrix membranes (MMMs) involve one type of polymer and one type of inorganic filler particle. Here, both polymer blending and MMM approaches are combined to form exceptional three-component membranes for CO2/N2 separation. Nano-sized amino-functionalized UiO-66 is added to a polymer blend of PIM-1 and an ether side chain functionalized polyphosphazene (MEEP80) to create a series of MMMs. Incorporation of UiO-66-NH2 particles boosts the CO2 permeability of the PIM-1/MEEP80 (75:25) blend from 3140 up to nearly 6000 Barrer, while maintaining its CO2/N2 selectivity within the range of 22–25, placing it well above the 2008 Robeson upper bound. In addition, the compatibility of the component parts leads to improved mechanical flexibility and mitigated physical aging for more than 300 days. This unique strategy constitutes a facile MMM formulation approach for energy efficient carbon capture from flue gas.
Haplotypes Spanning the Complement Factor H Gene Are Protective against Age-Related Macular Degeneration (2007)

Replication of the association between the protective haplotypes and decreased AMD susceptibility provides increased evidence that these associations have biological meaning. The suggestion of a haplotype-smoking interaction adds to the growing body of evidence that smoking is an important environmental covariate in AMD that should be considered in genetic studies. Identification of the protective variant(s) carried within these haplotypes is critical for understanding the etiology of AMD.
Effect of clay surface modification on the polymer nanocomposite foam structure (2004)

Nanoclay can work as a nucleation agent to control foam cell structure and reinforcement to enhance foam properties. In this paper, the clay surface is modified by a reactive quaternary ammonium surfactants and grafted with either poly(methyl methacrylate) (PMMA) or polystyrene (PS). The polystyrene and the polymer modified clay nanocomposites are synthesized by in-situ polymerization and extrusion compounding. By using CO 2 as the foaming agent, the nanocomposite foams are prepared in a single screw extruder. It is found that the surface modification has a great influence on the foam morphology. The presence of more CO 2 -philic PMMA on the clay surface leads to a lower melt viscosity.
Optimal Tuner Selection for Kalman Filter-Based Aircraft Engine Performance Estimation (2009)

A linear point design methodology for minimizing the error in on-line Kalman filter-based aircraft engine performance estimation applications is presented. This technique specifically addresses the underdetermined estimation problem, where there are more unknown parameters than available sensor measurements. A systematic approach is applied to produce a model tuning parameter vector of appropriate dimension to enable estimation by a Kalman filter, while minimizing the estimation error in the parameters of interest. Tuning parameter selection is performed using a multi-variable iterative search routine which seeks to minimize the theoretical mean-squared estimation error. This paper derives theoretical Kalman filter estimation error bias and variance values at steady-state operating conditions, and presents the tuner selection routine applied to minimize these values. Results from the application of the technique to an aircraft engine simulation are presented and compared to the conventional approach of tuner selection. Experimental simulation results are found to be in agreement with theoretical predictions. The new methodology is shown to yield a significant improvement in on-line engine performance estimation accuracy.
Selectable recombinant herpesvirus saimiri is capable of persisting in a human T-cell line (1989)

Strategies were developed to insert the neo resistance marker into the junction between L DNA and the right terminal repetitive H DNA of herpesvirus saimiri. Recombinant viruses were selectable in permissive epithelioid cultures. The human T-cell line Jurkat could be infected persistently with the Neor virus; the cells contained episomal viral DNA in high copy number. This selectable vector should be generally applicable for gene expression in human T cells.
<title>Perceptually tuned sub-band image coder</title> (1990)

In this paper we present a sub-band coder for true color images that uses an empirically derived perceptual masking model to set the allowable quantization noiselevel not only for each sub-band but also for each pixel in a given sub-band. The input image is converted into YIQ space and each channel is passed through a separable Generalized Quadrature Mirror Filterbank (GQMF). This separates the image's frequency content into into 4 equal width bands in both the horizontal and vertical dimension, resulting in a representation consisting of 16 sub-bands for each channel. Using this representation, a perceptual masking model is derived for each channel. The model incorporates spatial-frequency sensitivity, contrast sensitivity, and texture masking. Based on the image dependent information in each sub-band and the perceptual masking model, noise-level targets are computed for each point in a subband. These noise-level targets are used to set the quantization levels in a DPCM quantizer. The output from the DPCM quantizer is then encoded, using an entropybased coding scheme, in either lxi , 1x2, or 2x2 pixel parts, based on the the statistics in each 4x4 sub-block of a particular sub-band. One set of codebooks, consisting of 100,000 entries, is used for all images. A block elimination algorithm takes advantage of the peaky spatial energy distribution of sub-bands to avoid using bits for quiescent parts of a given sub-band. The resultant bitrate depends on the complexity of the input image. For the images we use, high quality output requires bitrates from 0.25 to 1 .25 bits/pixel, while nearly transparent quality requires 0.5 to 2.5 bits/pixel.
Influence of Grain Size of Non-oriented Electrical Steel Sheets on Iron Loss Deterioration by Shearing Process (2018)

The influence of the shearing process on the iron loss of non-oriented electrical steel sheets with the grain size of 10-155 µm was investigated. The ratio of iron loss deterioration showed a strong correlation with grain size of the material, and the deterioration ratio was smaller as the decrease of grain size. The smaller grain size material had a shorter droop height in the sheared edge, and the ratio of iron loss deterioration also had a good correlation with the droop height in the sheared edge. The effective plastic strain near the sheared edge calculated by elastic-plastic analysis based on FEM showed smaller values with a small material grain size.
Double blind, placebo controlled trial of oral lactoferrin in combination therapy for first line non-small cell lung cancer (NSCLC) (2005)

7141 Background: Recombinant human lactoferrin (rhLF) is a novel immunostimulatory agent with demonstrated anti-cancer activity in animals and NSCLC patients in Phase I/II trials. Oral rhLF has been administered to over 350 people and appears safe and well tolerated. We evaluated oral rhLF in combination with standard chemotherapy in first line NSCLC patients in this trial. Methods: 110 chemo-naive patients with advanced or metastatic NSCLC from eleven cancer centers were randomized to receive standard therapy (carboplatin + paclitaxel; C/P) plus either rhLF or placebo. C/P was administered in 3-week cycles. RhLF (or placebo) was administered orally, 1.5 g B.I.D., in 35-day cycles until radiological progression for a maximum of three cycles, starting the day following C/P dosing in cycles 1, 3 and 5. The primary end point is Best Overall Response (BOR) by CT using RECIST criteria. Secondary end points include Progression Free Survival (PFS) and Overall Survival by Kaplan-Meier curves and Quality of Life Assessments (EORTC QLQ C30, QLC LC 13) at Weeks 0, 6, 12, 18. Data will be unblinded for preliminary analysis in February 2005. Results: All 110 patients have been enrolled for over ten weeks. Study drug appears to be safe and well tolerated, with only one Grade 3/4 toxicity (abdominal pain) that is possibly rhLF/placebo related. 100 patients have had at least one post-therapy CT, and are evaluable for response rate (RR). So far, there have been 37 (37%) partial responses (PR) and an additional 53 patients (53%) had stable disease on their 6-week CT or later. Median PFS has not been reached. The five major published randomized trials evaluating 3-weekly first line C/P in Stage IIIB/IV NSCLC report an average RR of 25.9%. The 37% blended response rate observed in this trial is significantly better than that expected in this patient population. Conclusions: Oral rhLF is a safe and well-tolerated immunostimulatory drug. If the response rate of placebo patients in this study is consistent with the published literature, the blinded data suggests that rhLF may significantly enhance the response to first line C/P chemotherapy in advanced NSCLC without increasing toxicity. We will present unblinded data at ASCO. Author Disclosure Employment or Leadership Consultant or Advisory Role Stock Ownership Honoraria Research Funding Expert Testimony Other Remuneration Agennix
Cavity optomechanical sensors for atomic force microscopy (2011)

We develop a silicon cavity optomechanical sensor for atomic force microscopy through near-field coupling between a nanocantilever and microdisk cavity. The device exhibits sub-fm/ Hz displacement sensitivity, GHz bandwidth, and > 60 dB of dynamic range.
Antigen-specific T cell Redirectors: a nanoparticle based approach for redirecting T cells (2016)

Redirection of T cells to target and destroy tumors has become an important clinical tool and major area of research in tumor immunology. Here we present a novel, nanoparticle-based approach to selectively bind antigen-specific cytotoxic T cells (CTL) and redirect them to kill tumors, termed ATR (Antigen-specific T cell Redirectors). ATR were generated by decorating nanoparticles with both an antigen-specific T cell binding moiety, either peptide loaded MHC-Ig dimer or clonotypic anti-TCR antibody, and a model tumor cell binding moiety, anti-CD19 antibody to engage CD19+ tumor cells. ATR stably bind tumor cells and CTL in a dose dependent fashion and stimulate antigen-specific conjugate formation between those cells. ATR induced redirected lysis of tumor cells in vitro, as demonstrated by 51Cr-release killing. In vivo ATR administration led to reduced tumor growth in a SCID/beige human lymphoma treatment model. In summary, ATR represent a novel, nanoparticle based approach for redirecting antigen-specific CTL to kill tumors.
A study on the aging of ultra-thin Palladium films on SAW hydrogen gas sensors (2010)

Traditionally, low-powered, room temperature sensing of gaseous hydrogen (H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> ) is difficult. With renewed interest in H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> as a source of energy, there is a need for reliable, energy-efficient sensors. A potential solution can be found in using surface acoustic wave (SAW) devices, which have been implemented as passive, wireless RFID tag-sensors. Thus, in concept, it is advantageous to develop a SAW device with H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> sensing capabilities. Prior experiments have successfully demonstrated a passive SAW-based H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas sensor by placing an ultra-thin Palladium (Pd) film (<;50 Å) in the propagation path. These sensors have an instantaneous response and a significant fractional change in SAW propagation loss; however, the lifetime of these sensors are still unknown. Hence, the objective of this study was to examine the influence of aging of ultra-thin Pd films on the usable life of passive SAW H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas sensors. The aging behavior of a thin film is highly dependent on its morphology and the environment in which it is used. Particularly, during growth, ultra-thin Pd films may form a discontinuous network of nano-sized atomic islands-nano-clusters. These nano-clusters may be amorphous or have a highly defective crystalline structure. When used in ambient air (1atm, 79% N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , 21% O <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> , 44% humidity, 21°C), these films are susceptible to oxygen adsorption (i.e., blocking H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> sorption and decreasing the H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> reactivity of the film), which reduces the useable life of the sensor. This paper presents data demonstrating that ultra-thin Pd films suffer from oxygen adsorption when exposed to ambient air. The results of the study provide promising solutions to the aging problem, such as encapsulation and film annealing. These solutions may accelerate the practical implementation of passive, wireless, SAW H <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">2</sub> gas sensors in various environments.
Epitope Mapping of the Immunodominant Antigen TB10.4 and the Two Homologous Proteins TB10.3 and TB12.9, Which Constitute a Subfamily of the <i>esat-6</i> Gene Family (2002)

The human T-cell recognition of the low-molecular-mass culture filtrate antigen TB10.4 was evaluated in detail. The molecule was strongly recognized by T cells isolated from tuberculosis (TB) patients and from BCG-vaccinated donors. The epitopes on TB10.4 were mapped with overlapping peptides and found to be distributed throughout the molecule. The broadest response was found in TB patients, whereas the response in BCG-vaccinated donors was focused mainly toward a dominant epitope located in the N terminus (amino acids 1 to 18). The gene encoding TB10.4 was found to belong to a subfamily within the esat-6 family that consists of the three highly homologous proteins TB10.4, TB10.3, and TB12.9 (Rv0288, Rv3019c, and Rv3017c, respectively). Southern blot analysis combined with database searches revealed that the three members of the TB10.4 family were present only in strains of the Mycobacterium tuberculosis complex, including BCG, and M. kansasii, whereas other atypical mycobacteria had either one (M. avium, M. intracellulare, and M. marinum) or none (M. scrofulaceum, M. fortuitum, and M. szulgai) of the genes. The fine specificity of the T-cell response to the three closely related esat-6 family members was markedly different, with only a few epitopes shared between the molecules. Minimal differences in the amino acid sequence translated into large differences in recognition by T cells and secretion of gamma interferon. In general, the peptides from TB10.4 stimulated the largest responses, but epitopes unique to both TB10.3 and TB12.9 were found. The relevance of the findings for TB vaccine development and as a potential mechanism for immune evasion is discussed.
Detection of Perchlorate Anion on Functionalized Silver Colloids Using Surface-Enhanced Raman Scattering (2005)

Perchlorate anion interferes with the uptake of iodide by the human thyroid gland and consequently disrupts the regulation of metabolism. Chronic exposure to high levels of perchlorate may lead to the formation of thyroid gland tumors. Although the Environmental Protection Agency (EPA) has not set a maximum contaminant level (MCL) for perchlorate, a draft drinking water range of 4-18 ppb based on 2 liter daily consumption of water has been established. The current EPA approved method for detecting perchlorate uses ion chromatography which has a detection limit of ~1ppb and involves lengthy analytical time in the laboratory. A unique combination of the surface-enhanced Raman scattering (SERS) effect and the bifunctional anion exchange resin’s high selectivity may provide an alternative way to detect perchlorate at such low concentrations and with high specificity. SERS, which uses laser excitation of adsorbed perchlorate anions on silver nanoparticles, has been shown to detect perchlorate anions at concentrations as low as 50 ppb. Normal micro-Raman analysis of perchlorate sorbed onto the resin beads has detected an even lower concentration of 10 ppb. In an effort to integrate these two effects, silver nanoparticles were coated with N-trimethoxysilylpropyl-N,N,N-trimethylammonium chloride, a functional group similar to that found on the resin bead, and subsequently inserted into different perchlorate concentration environments. This method has resulted in perchlorate detection down to ~10 ppb and a more consistent detection of perchlorate anion at ~50 ppb than that of earlier methods. As suggested by the direct insertion of functionalized silver colloids into perchlorate samples, this technique may potentially allow for the development of a probe using on-site Raman spectrometry to detect significantly low concentrations of perchlorate in situ rather than in the laboratory.
8.6% Efficient CZTSSe Solar Cells Sprayed from Water–Ethanol CZTS Colloidal Solutions (2014)

Copper zinc tin sulfide-selenide, Cu2ZnSn(S1-xSex)4 (CZTSSe), thin film photovoltaic devices were fabricated using a fast and environmentally friendly preparation method, consisting of the following steps: An instantaneous synthesis of a Cu-Zn-Sn-S (no Se) colloid, a nonpyrolytic spray of a dispersion of this colloid in a water-ethanol mixture, and a sequential annealing first in a N2 atmosphere and second in a Se atmosphere. The achievement of cell efficiencies up to 8.6% under AM1.5G (cell area 0.25 cm(2)) and without antireflecting coating indicates that this method can compete with other vacuum-based or more complex wet deposition methods.