gebhart/patrepeval huggingface dataset:
Development and evaluation of an exact fan‐beam reconstruction algorithm using an equal weighting scheme via locally compensated filtered backprojection (LCFBP) (2006)

A novel exact fan-beam image reconstruction formula is presented and validated using both phantom data and clinical data. This algorithm takes the form of the standard ramp filtered backprojection (FBP) algorithm plus local compensation terms. This algorithm will be referred to as a locally compensated filtered backprojection (LCFBP). An equal weighting scheme is utilized in this algorithm in order to properly account for redundantly measured projection data. The algorithm has the desirable property of maintaining a mathematically exact result for: the full scan mode (2pi), the short scan mode (pi+ full fan angle), and the supershort scan mode [less than (pi+ full fan angle)]. Another desirable feature of this algorithm is that it is derivative-free. This feature is beneficial in preserving the spatial resolution of the reconstructed images. The third feature is that an equal weighting scheme has been utilized in the algorithm, thus the new algorithm has better noise properties than the standard filtered backprojection image reconstruction with a smooth weighting function. Both phantom data and clinical data were utilized to validate the algorithm and demonstrate the superior noise properties of the new algorithm.
Ala(0)-actagardine, a New Lantibiotic from Cultures of Actinoplanes liguriae ATCC 31048. (1999)

The actagardine-producing strain Actinoplanes liguriae ATCC 31048, forms an additional lantibiotic when it is cultured on mannitol and soya meal. The new compound, Ala(0)-actagardine (1), has been isolated by solid-phase extraction followed by a two-step chromatographic separation. The molecular formula of 1 is C84H129N21O25S4. Its chemical structure was determined by 2D-NMR analysis and was further confirmed by an amino acid analysis, Edman degradation, and partial synthesis from actagardine. 1 exhibits a slightly higher biological activity than the parent compound actagardine. The synthetic analogs Lys(0)-actagardine (2) and Ile(0)-actagardine (3) demonstrate also antibacterial activities and emphasize the importance of the N-terminus for further derivatization.
Functional immunoglobulin E cross-reactivity between Pas n 1 of Bahia grass pollen and other group 1 grass pollen allergens (2011)

Background Grass pollens are major triggers of allergic rhinitis and asthma, but the immunological relationships between pollen allergens of the subtropical Bahia grass, Paspalum notatum, and temperate grasses are unresolved.
Molecularly imprinted polymer sensors for detection in the gas, liquid, and vapor phase (2012)

Fast, reliable, and inexpensive analytical techniques for detection of airborne chemical warfare agents are desperately needed. Recent advances in the field of molecularly imprinted polymers have created synthetic nanomaterials that can sensitively and selectively detect these materials in aqueous environments, but thus far, they have not been demonstrated to work for detection of vapors. The imprinted polymers function by mimicking the function of biological receptors. They can provide high sensitivity and selectivity but, unlike their biological counterparts, maintain excellent thermal and mechanical stability. The traditional imprinted polymer approach is further enhanced in this work by the addition of a luminescent europium that has been introduced into the polymers to provide enhanced chemical affinity as well as a method for signal transduction to indicate the binding event. The europium in these polymers is so sensitive to the bound target; it can distinguish between species differing by a single methyl group. The imprinted polymer technology is fiber optic-based making it inexpensive and easily integratable with commercially available miniature fiber optic spectrometer technologies to provide a shoebox size device. In this work, we will describe efforts to apply these sensors for detection of airborne materials and vapors. Successful application of this technology will provide accurate low level vapor detection of chemical agents or pesticides with little to no false positives.
Differentiation of <i>Pseudomonas aeruginosa</i> into the alginate‐producing form: inactivation of <i>mucB</i> causes conversion to mucoidy (1993)

Mucoidy in Pseudomonas aeruginosa is a critical virulence factor associated with chronic respiratory infections in cystic fibrosis. A cluster of three tightly linked genes, algU, mucA and mucB located at 67.5 min, controls development of mucoid phenotype. This locus is allelic with a group of mutations (muc) associated with conversion into constitutively mucoid forms. One of the genes previously characterized in this region, algU, is absolutely required for the transcriptional activation of algD, a critical event in the establishment of mucoidy. AlgU is homologous to the alternative sigma factor sigma H (Spo0H) controlling sporulation and competence in Bacillus. Two genes downstream of algU, mucA and mucB were further characterized in this study. Previous complementation studies have demonstrated that mucA is required for suppression of mucoidy in the muc-2 strain PAO568. In this work, complementation analysis indicated that, in addition, mucB was required for suppression of mucoidy in the muc-25 strain PAO581, and for enhanced complementation of the muc-2 mutation in PAO568. The complete nucleotide sequence of mucA and mucB was determined. Insertional inactivation of mucB on the chromosome of the standard genetic strain PAO resulted in mucoid phenotype, and in a strong transcriptional activation of algD. Thus, a loss of mucB function is sufficient to cause conversion of P. aeruginosa into the mucoid phenotype. Since the algU-mucA-mucB region is a general site where muc mutations have been mapped, it is likely that mucB participates in the emergence of mucoid forms. Both mucA and mucB play a regulatory role in concert with the sigma-like factor AlgU; all three genes, along with signal transduction and histone-like elements, control differentiation of P. aeruginosa into the mucoid phenotype.
Single-layer graphene cathodes for organic photovoltaics (2011)

A laminated single-layer graphene is demonstrated as a cathode for organic photovoltaic devices. The measured properties indicate that graphene offers two potential advantages over conventional photovoltaic electrode materials; work function matching via contact doping, and increased power conversion efficiency due to transparency. These findings indicate that flexible, light-weight all carbon solar cells can be constructed using graphene as the cathode material.
Study on thermal annealing of cadmium zinc telluride (CZT) crystals (2010)

Cadmium Zinc Telluride (CZT) has attracted increasing interest with its promising potential as a room-temperature nuclear-radiation-detector material. However, different defects in CZT crystals, especially Te inclusions and dislocations, can degrade the performance of CZT detectors. Post-growth annealing is a good approach potentially to eliminate the deleterious influence of these defects. At Brookhaven National Laboratory (BNL), we built up different facilities for investigating post-growth annealing of CZT. Here, we report our latest experimental results. Cd-vapor annealing reduces the density of Te inclusions, while large temperature gradient promotes the migration of small-size Te inclusions. Simultaneously, the annealing lowers the density of dislocations. However, only-Cd-vapor annealing decreases the resistivity, possibly reflecting the introduction of extra Cd in the lattice. Subsequent Te-vapor annealing is needed to ensure the recovery of the resistivity after removing the Te inclusions.
Direct Detection and Magnetic Isolation of <i>Chlamydia trachomatis</i> Major Outer Membrane Protein-Specific CD8+ CTLs with HLA Class I Tetramers (2000)

We recently identified HLA class I-presented epitopes in the major outer membrane protein (MOMP) of Chlamydia trachomatis that elicit CTL responses in human genital tract infections. T cells possessing cytolytic activities specific for these epitopes could be detected following in vitro stimulation of peripheral blood CD8(+) T cells with peptides. In the present study we used HLA-A2 tetramers for detailed characterization of MOMP-specific CTL responses. Ex vivo tetramer analysis detected MOMP-specific T cells in the peripheral blood of infected individuals at significant frequencies (0.01-0.20% of CD8(+) T cells). After in vitro stimulation with peptides, the frequencies of MOMP peptide-specific T cells increased up to 2.34% of CD8(+) T cells in bulk cultures. In contrast, HLA-A2/MOMP tetramer-binding T cells were virtually undetectable in the peripheral blood from uninfected individuals, either ex vivo or after 3 wk of in vitro peptide stimulation of their T cells. Magnetically sorted, tetramer-bound T cells specifically lysed peptide-pulsed targets as well as C. trachomatis-infected epithelial cells with nearly 50-fold greater per cell efficiency than that of unsorted populations. This study provides conclusive evidence of in vivo induction of HLA class I-restricted CD8(+) CTL responses to C. trachomatis MOMP. Direct detection of these cells with tetramers will allow their further characterization without prior manipulation and facilitate monitoring of CTL responses during infections and in immunization trials with MOMP-based vaccines.
Engineering a Novel Antibody-Peptide Bispecific Fusion Protein Against MERS-CoV (2019)

In recent years, tremendous efforts have been made in the engineering of bispecific or multi-specific antibody-based therapeutics by combining two or more functional antigen-recognizing elements into a single construct. However, to the best of our knowledge there has been no reported cases of effective antiviral antibody-peptide bispecific fusion proteins. We previously developed potent fully human monoclonal antibodies and inhibitory peptides against Middle East Respiratory Syndrome Coronavirus (MERS-CoV), a novel coronavirus that causes severe acute respiratory illness with high mortality. Here, we describe the generation of antibody-peptide bispecific fusion proteins, each of which contains an anti-MERS-CoV single-chain antibody m336 (or normal human IgG1 CH3 domain as a control) linked with, or without, a MERS-CoV fusion inhibitory peptide HR2P. We found that one of these fusion proteins, designated as m336 diabody-pep, exhibited more potent inhibitory activity than the antibody or the peptide alone against pseudotyped MERS-CoV infection and MERS-CoV S protein-mediated cell-cell fusion, suggesting its potential to be developed as an effective bispecific immunotherapeutic for clinical use.
Thermomagnetic control of the operating point of magnetic fusion reactors (1981)

Control of the power output of tokamak reactors is proposed through use of materials whose magnetic properties depend upon the operating temperature. By varying this temperature, such materials, when located between the plasma and the magnets that produce the confining fields, control the deviation from axisymmetry of the magnetic fields in the plasma and hence control the operating point of the device.
An Online Self-Tunable Method to Denoise CGM Sensor Data (2009)

Continuous glucose monitoring (CGM) devices can be very useful in diabetes management. Unfortunately, their use in online applications, e.g., for hypo/hyperalert generation, is made difficult by random noise measurement. Remarkably, the SNR of CGM data varies with the sensor and with the individual. As a consequence, approaches in which filter parameters are not allowed to adapt to the current SNR are likely to be suboptimal. In this paper, we present a new online methodology to reduce noise in CGM signals by a Kalman filter (KF), whose unknown parameters are adjusted in a given individual by a stochastically based smoothing criterion exploiting data of a burn-in interval. The performance of the new KF approach is quantitatively assessed on Monte Carlo simulations and 24 real CGM datasets. Our results are compared with those obtained by a moving-average (MA) filtering approach with fixed parameters currently in use in likely all commercial CGM devices. Results show that the new KF approach performs much better than MA. For instance, on real data, for comparable signal denoising, the delay introduced by KF is about 35% less than that obtained by MA.
Efficient scalable production of therapeutic microvesicles derived from human mesenchymal stem cells (2018)

Microvesicles (MVs) released by cells are involved in a multitude of physiological events as important mediators of intercellular communication. MVs derived from mesenchymal stem cells (MSCs) contain various paracrine factors from the cells that primarily contribute to their therapeutic efficacy observed in numerous clinical trials. As nano-sized and bi-lipid layered vesicles retaining therapeutic potency equivalent to that of MSCs, MSC-derived MVs have been in focus as ideal medicinal candidates for regenerative medicine, and are preferred over MSC infusion therapy with their improved safety profiles. However, technical challenges in obtaining sufficient amounts of MVs have limited further progress in studies and clinical application. Of the multiple efforts to reinforce the therapeutic capacity of MSCs, few studies have reportedly examined the scale-up of MSC-derived MV production. In this study, we successfully amplified MV secretion from MSCs compared to the conventional culture method using a simple and efficient 3D-bioprocessing method. The MSC-derived MVs produced in our dynamic 3D-culture contained numerous therapeutic factors such as cytokines and micro-RNAs, and showed their therapeutic potency in in vitro efficacy evaluation. Our results may facilitate diverse applications of MSC-derived MVs from the bench to the bedside, which requires the large-scale production of MVs.
Three-dimensional image encryption, transmission, and processing by using digital holography (2005)

We describe several methods for optoelectronic processing of 3D images based in digital holography. In all cases, phase-shift digital holography is used to record the complex amplitude distribution associated to the diffraction field generated by 3D objects illuminated with coherent light. First, we review a technique to encrypt a 3D image by using digital holography. Encryption is performed by using random phase codes as key functions. In this way, it is possible to send secure 3D information through conventional digital communication lines. In our approach, decryption is carried out digitally. Next we describe both, digital and optical reconstruction of 3D images starting from digital holograms. Finally, we show how to perform 3D pattern recognition with high discrimination based in the above techniques. Experimental results are presented.
Completion of a Truncated Attenuation Image From the Attenuated PET Emission Data (2012)

Positron emission tomographs (PETs) are currently almost exclusively designed as hybrid systems. The current standard is the PET/CT combination, while prototype PET/MRI systems are being studied by several research groups. One problem in these systems is that the transaxial field-of-view of the second system is smaller than that of the PET camera and does not provide complete attenuation data. Because this second system provides the image for PET attenuation and scatter correction, the smaller FOV causes truncation of the attenuation map, producing bias in the attenuation corrected activity image. In this paper, we propose a maximum-a-posteriori algorithm for estimating the missing part of the attenuation map from the PET emission data. The method is evaluated on five artificially truncated 18F-FDGPET/CT studies, where it reduced the error on the reconstructed PET activities from 20% to less than 7%. The results on a PET/MRI patient study with 18F-FDG are presented as well.
Optimization of the Extrusion Process for Glass-Fiber-Reinforced Tubes (1995)

The resistance of short-fiber-reinforced thermoplastic tubes to internal pressure is strongly related to fiber orientation. A new way to increase the degree of orientation in the hoop direction is presented. It consists of injecting a lubricant at the surface of a diverging die. A calculation of flow and fiber orientation in a lubricated die with a divergent final land shows that extensional deformations, which tend to orient the fibers perpendicular to the flow, take place on the entire thickness; in contrast, without lubricant, shear deformations near the surface orient the fibers in the flow direction. Various dies are tested with a 30 wt% short-glass-fiber-reinforced polypropylene. Observations show that, with the lubricated diverging die, the fibers are oriented mainly in the hoopwise direction throughout the tube thickness. Consequently, mechanical properties are increased in this direction. The resistance of the tube is increased by about 40%.
Age and Diet Affect Genetically Separable Secondary Injuries that Cause Acute Mortality Following Traumatic Brain Injury in <i>Drosophila</i> (2016)

Outcomes of traumatic brain injury (TBI) vary because of differences in primary and secondary injuries. Primary injuries occur at the time of a traumatic event, whereas secondary injuries occur later as a result of cellular and molecular events activated in the brain and other tissues by primary injuries. We used a Drosophila melanogaster TBI model to investigate secondary injuries that cause acute mortality. By analyzing mortality percentage within 24 hr of primary injuries, we previously found that age at the time of primary injuries and diet afterward affect the severity of secondary injuries. Here, we show that secondary injuries peaked in activity 1-8 hr after primary injuries. Additionally, we demonstrate that age and diet activated distinct secondary injuries in a genotype-specific manner, and that concurrent activation of age- and diet-regulated secondary injuries synergistically increased mortality. To identify genes involved in secondary injuries that cause mortality, we compared genome-wide mRNA expression profiles of uninjured and injured flies under age and diet conditions that had different mortalities. During the peak period of secondary injuries, innate immune response genes were the predominant class of genes that changed expression. Furthermore, age and diet affected the magnitude of the change in expression of some innate immune response genes, suggesting roles for these genes in inhibiting secondary injuries that cause mortality. Our results indicate that the complexity of TBI outcomes is due in part to distinct, genetically controlled, age- and diet-regulated mechanisms that promote secondary injuries and that involve a subset of innate immune response genes.
Simultaneous targeting of interleukin-1 and interleukin-18 is required for protection against inflammatory and septic shock (2014)

Sepsis is one of the leading causes of death around the world. The failure of clinical trials to treat sepsis demonstrates that the molecular mechanisms are multiple and still insufficiently understood. The objective is to clarify the long disputed hierarchical contribution of several central inflammatory mediators, namely IL-1β, IL-18, CASP7, CASP1 and CASP11, in septic shock, and to explore their therapeutic potential.
Key Developments in Stem Cell Therapy in Cardiology (2012)

A novel therapeutic strategy to prevent or reverse ventricular remodeling, the substrate for heart failure and arrhythmias following a myocardial infarction, is the use of cell-based therapy. Successful cell-based tissue regeneration involves a complex orchestration of cellular and molecular events that include stem cell engraftment and differentiation, secretion of anti-inflammatory and angiogenic mediators, and proliferation of endogenous cardiac stem cells. Recent therapeutic approaches involve bone marrow-derived mononuclear cells and mesenchymal stem cells, adipose tissue-derived stem cells, cardiac-derived stem cells and cell combinations. Clinical trials employing mesenchymal stem cells and cardiac- derived stem cells have demonstrated efficacy in infarct size reduction and regional wall contractility improvement. Regarding delivery methods, the safety of catheter-based, transendocardial stem cell injection has been established. These proof-of-concept studies have paved the way for ongoing pivotal trials. Future studies will focus on determining the most efficacious cell type(s) and/or cell combinations and the mechanisms underlying their therapeutic effects.
Nitrile hydratase of Pseudomonas chlororaphis B23 (1987)

Nitrile hydratase of Pseudomonas chlororaphis B23 was completely stabilized by the addition of 22 mM n-butyric acid. The enzyme was purified from extracts of methacrylamide-induced cells of P. chlororaphis B23 in eight steps. At the last step, the enzyme was crystallized by adding ammonium sulfate. The crystallized enzyme appeared to be homogeneous from analysis by polyacrylamide gel electrophoresis, analytical ultracentrifuge, and double diffusion in agarose. The enzyme has a molecular mass of about 100 kDa and consists of four subunits identical in molecular mass (approximately 25 kDa). The enzyme contained approximately 4 mol iron/mol enzyme. The concentrated solution of highly purified nitrile hydratase had a pronounced greyish green color and exhibited a broad absorption in visible range with a absorption maxima at 720 nm. A loss of enzyme activity occurred in parallel with the disappearance of the absorption in the visible range under a variety of conditions. The enzyme catalyzed stoichiometrically the hydration of nitrile to amide, and no formation of acid and ammonia were detected. The enzyme was active toward various aliphatic nitriles, particularly, nitriles with 3-6 carbon atoms, e.g. propionitrile, n-butyronitrile, acrylonitrile and cyclopropyl cyanide, served as the most suitable substrates.
Experimental and Numerical Study on CO<sub>2</sub> Sweep Volume during CO<sub>2</sub> Huff-n-Puff Enhanced Oil Recovery Process in Shale Oil Reservoirs (2019)

CO2 huff-n-puff has been proven to be the most effective enhanced oil recovery (EOR) method in shale oil reservoirs. The injected CO2 will replenish reservoir energy and penetrate the reservoir matrix to extract oil. However, the CO2 sweep volume during the huff-n-puff process has not been accurately evaluated by existing studies. In this paper, the CO2 sweep volume was investigated through experimental and numerical simulation methods. In the experimental study, the CO2 sweep areas were depicted by X-ray computed tomography scan technology. The results indicated that the ratio of the CO2 sweep area was 78.63% in the seventh huff-n-puff cycle, leading to a total oil recovery of 56.80%. The numerical simulation considered the mechanisms of molecular diffusion and nanopore confinement. The results showed that in the first huff-n-puff cycle, the gas sweep volume percentage was 9.47% after 100 days of huff period. In the gas swept volume, oil viscosity was reduced by 25.9% to 68.2%. After three cycles of CO2 injection, the oil recovery manifested a 1.5% increase compared to the case without huff-n-puff. The contributions of different parameters on gas sweep volume and cumulative oil recovery were investigated. The results illustrated that the nanopore confinement effect and molecular diffusion had significant impacts on the gas sweep volume and cumulative oil recovery. Higher injection pressure, longer huff time, and more huff-n-puff cycles lead to larger gas sweep volume, as well as cumulative oil recovery. A suitable primary depletion period and a huff-n-puff schedule should be determined based on the requirements of field production. The investigations in this study provide insights into better understanding of the EOR mechanisms and optimizing the design of CO2 huff-n-puff operations in shale oil reservoirs.
Rapid and Simple Platelet Function Assay to Assess Glycoprotein IIb/IIIa Receptor Blockade (1997)

A simple and rapid assay sensitive to GP IIb/IIIa receptor blockade has been developed that may be helpful in optimizing GP IIb/IIIa antagonist therapy.