gebhart/patrepeval huggingface dataset:
T‐Cell Receptor V‐Gene Usage in Synovial Fluid and Synovial Tissue from RA Patients (1992)

The question of whether there is a preferential use of certain V genes in T cells entering an inflamed joint has hitherto been studied mainly using unfractionated cells from synovial fluid and tissue respectively, and no clear answer to the question has yet been provided. Concomitantly, evidence has been provided that the use of V genes may differ considerably between CD4+ and CD8+ T cells, and consequently that detection of biased V-gene expression within an inflammatory lesion may require separate analysis of the two T-cell subsets. In this paper we have therefore studied T-cell receptor V-gene expression in rheumatoid arthritis by means of double stainings of synovial fluid and blood for available anti-TCR monoclonal antibodies and antibodies to CD4 and CD8, respectively. Double stainings were also performed with anti-TCR antibodies and antibodies to activation markers HLA-DR and IL-2R. A certain bias towards the preferential use of certain V genes was seen particularly in the synovial fluid samples within both the CD4+ and CD8+ T-cell populations, but no uniform pattern was evident among the 35 patients investigated.
Noninvasive radiomics signature based on quantitative analysis of computed tomography images as a surrogate for microvascular invasion in hepatocellular carcinoma: a pilot study (2017)

We explore noninvasive biomarkers of microvascular invasion (mVI) in patients with hepatocellular carcinoma (HCC) using quantitative and semantic image features extracted from contrast-enhanced, triphasic computed tomography (CT). Under institutional review board approval, we selected 28 treatment-naive HCC patients who underwent surgical resection. Four radiologists independently selected and delineated tumor margins on three axial CT images and extracted computational features capturing tumor shape, image intensities, and texture. We also computed two types of "delta features," defined as the absolute difference and the ratio computed from all pairs of imaging phases for each feature. 717 arterial, portal-venous, delayed single-phase, and delta-phase features were robust against interreader variability ([Formula: see text]). An enhanced cross-validation analysis showed that combining robust single-phase and delta features in the arterial and venous phases identified mVI (AUC [Formula: see text]). Compared to a previously reported semantic feature signature (AUC 0.47 to 0.58), these features in our cohort showed only slight to moderate agreement (Cohen's kappa range: 0.03 to 0.59). Though preliminary, quantitative analysis of image features in arterial and venous phases may be potential surrogate biomarkers for mVI in HCC. Further study in a larger cohort is warranted.
Chitosan Sponges to Locally Deliver Amikacin and Vancomycin: A Pilot In Vitro Evaluation (2010)

Chitosan sponges may provide a potential local drug delivery device for preventing musculoskeletal infections.
Management of primary cutaneous melanoma of the head and neck: The University of Colorado experience and a review of the literature (2001)

There is no clear indication that either ELND or adjuvant radiation therapy impacts on the outcome of patients with primary melanoma of the head and neck. Sentinel lymph node biopsy, in appropriate cases, is becoming the standard of care.
ChemInform Abstract: CHEMIE DER BORANE 16. MITT. OPTISCHE ISOMERIE IN DER DEKABORANREIHE (1970)

Abstract Triphenylsilylmanganpentacarbonyl (I) setzt sich mit aliphatischen oder aromatischen Phosphiten (II) zu einem Gemisch der Spaltprodukte (III) und (IV) um.
Melt flow and strength of branched styrene copolymers (1967)

Abstract In order to assess the dependence of strength properties of glassy polymers upon the extent of branching, copolymers of poly(styrene–acrylonitrile) were prepared. By using principally three methods: ( a ) hydroperoxide intermediates, ( b ) hydroxyl radical initiation, and ( c ) incorporation of transfer monomers, branched polymers with high levels of branching with comb and dendritic type structures were generated. The tensile strength was found to be strongly correlatable with melt flow, and, in general, the branched copolymers were found to have the same tensile strength as linear polymers of the same melt index.
Antibiotic Trapping by Plasmid-Encoded CMY-2 β-Lactamase Combined with Reduced Outer Membrane Permeability as a Mechanism of Carbapenem Resistance in Escherichia coli (2013)

A liver transplant patient was admitted with cholangitis, for which meropenem therapy was started. Initial cultures showed a carbapenem-susceptible (CS) Escherichia coli strain, but during admission, a carbapenem-resistant (CR) E. coli strain was isolated. Analysis of the outer membrane protein profiles showed that both CS and CR E. coli lacked the porins OmpF and OmpC. Furthermore, PCR and sequence analysis revealed that both CS and CR E. coli possessed bla(CTX-M-15) and bla(OXA-1). The CR E. coli strain additionally harbored bla(CMY-2) and demonstrated a >15-fold increase in β-lactamase activity against nitrocefin, but no hydrolysis of meropenem was detected. However, nitrocefin hydrolysis appeared strongly inhibited by meropenem. Furthermore, the CMY-2 enzyme demonstrated lower electrophoretic mobility after its incubation either in vitro or in vivo with meropenem, indicative of its covalent modification with meropenem. The presence of the acyl-enzyme complex was confirmed by mass spectrometry. By transformation of the CMY-2-encoding plasmid into various E. coli strains, it was established that both porin deficiency and high-level expression of the enzyme were needed to confer meropenem resistance. In conclusion, carbapenem resistance emerged by a combination of elevated β-lactamase production and lack of porin expression. Due to the reduced outer membrane permeability, only small amounts of meropenem can enter the periplasm, where they are trapped but not degraded by the large amount of the β-lactamase. This study, therefore, provides evidence that the mechanism of "trapping" by CMY-2 β-lactamase plays a role in carbapenem resistance.
Separate vertical wiring for the fixation of comminuted fractures of the inferior pole of the patella (2003)

Comminuted and displaced fractures of the inferiorole of the patella are not easy to reduce and it is difficult to fix the fragments soundly enough to allow early movement of the knee. We have evaluated the clinical effectiveness of the separate vertical wiring technique in acute comminuted fractures of the inferior pole of the patella. A biomechanical study was also performed using ten pairs of embalmed cadaver knees. A four-part fracture was made on the inferior pole of the patella and fixed by two separate vertical wires on one side and two pull-out sutures after partial patellectomy on the other. The ultimate load to failure in the first group was significantly higher than in the second (250.1+/- 109.7 N v 69.7 +/- 18.9 N, p < 0.002), as was the stiffness (279.9 +/- 76.4 N/mm v 23.2 +/- 11.4 N/mm, p < 0.001). The separate wire technique was used in 25 patients with comminuted fractures of the inferior pole of the patella who were followed up for a mean period of 22 months (10 to 50). All the fractures healed at a mean of seven weeks (6 to 10). No breakage of a wire or infection occurred. The mean grading at the final follow-up was 29.5 points (27 to 30) using the Böstman method. This technique preserved the length of the patella, fixed the comminuted fragments of the inferior pole and avoided long-term immobilisation of the knee.
Characterizing protein structures by surface mapping (2008)

As the availability of protein crystallographic structures grows, new methods are needed to characterize, compare, and interpret crystal structure data. Surface geometry is important in molecular function, as interactions with other molecules in the cell happen at the protein surface. This dissertation describes a method of mapping and comparing surfaces of crystallographic structures, using the protein kinase family as a model. Pockets are rapidly computed using two pieces of software, FADE and Crevasse. FADE uses gradients of atomic density to locate grooves and pockets on the molecular surface. Crevasse, a new piece of software, segments the FADE output into distinct pockets that can be used in computations. A map of pockets on the catalytic core of Protein Kinase A shows the ATP and peptide docking sites, locations for C-helix anchoring, the myristylation site, and sites for regulatory subunit interaction. There are other sites identified where Protein Kinase A is likely to interact with other proteins, but the binding partners have not been identified. Spatially clustering pockets across a family of aligned proteins can identify similarities and differences within the family. In the set of ten kinase cores studied, differences in the active site cleft between serine/ threonine and tyrosine kinases are visible. Shared mechanisms of C-helix anchoring are also evident, and a novel site at the top of the N-lobe is present in all the kinases. There are other pockets on the kinases that are strongly conserved but have not yet been mapped to a protein-protein interaction
Activated Transport in Magnetic-Field Induced Insulating Phase in Two-Dimensional Electron Gas in InGaAs/InP Heterostructures (1997)

We report on experiments on low temperature (millikelvin range) activated magnetotransport on low-density two-dimensional electron systems in InGaAs/In for Landau level filling factors 0.25 < v < 0.55. The activation energy increases approximately linearly with decreasing filling factor. The observations are discussed in the light of the formation of the Wigner solid.
Supercritical Fluid (Dense Gas) Chromatography/Extraction with Linear Density Programming (1982)

Abstract The versatility of dense gases or supercritical fluids as solvents is briefly reviewed., It is pointed out that gas density is the key parameter controlling solvent power and it is argued that density programming should replace pressure programming for chro-matographlc and extractive separations. Our previous theory of dense gas solubility and solubility thresholds is then used to explain why relatively high pressures are desirable for dense gas separations. The theory is also used to examine peak spacing for linear density programs to develop a speeial density program for uniform peak spacing. An experimental linear density programming system utilizing CO2 at 40 C and at pressures up to 300 atmospheres is described and factors affecting separation efficiency are evaluated. A separation of four aromatic compounds is demonstrated using programmed density extraction alone. Chromatographic columns used with polystyrene oligomers and polynuclear aromatic compounds are shown to improve the separation. The spacing of oligomers is shown to be in qualitative accord with theory. Finally, factors to be considered in optimum programming are discussed.
Functional expression of aryl‐alcohol oxidase in <i>Saccharomyces cerevisiae</i> and <i>Pichia pastoris</i> by directed evolution (2018)

Aryl-alcohol oxidase (AAO) plays a fundamental role in the fungal ligninolytic secretome, acting as a supplier of H<sub>2</sub> O<sub>2</sub> . Despite its highly selective mechanism of action, the presence of this flavooxidase in different biotechnological settings has hitherto been hampered by the lack of appropriate heterologous expression systems. We recently described the functional expression of the AAO from Pleurotus eryngii in Saccharomyces cerevisiae by fusing a chimeric signal peptide (preαproK) and applying structure-guided evolution. Here, we have obtained an AAO secretion variant that is readily expressed in S. cerevisiae and overproduced in Pichia pastoris. First, the functional expression of AAO in S. cerevisiae was enhanced through the in vivo shuffling of a panel of secretion variants, followed by the focused evolution of the preαproK peptide. The outcome of this evolutionary campaign-an expression variant that accumulated 4 mutations in the chimeric signal peptide, plus two mutations in the mature protein- showed 350-fold improved secretion (4.5 mg/L) and was stable. This secretion mutant was cloned into P. pastoris and fermented in a fed-batch bioreactor to enhance production to 25 mg/L. While both recombinant AAO from S. cerevisiae and P. pastoris were subjected to the same N-terminal processing and had a similar pH activity profile, they differed in their kinetic parameters and thermostability. The strong glycosylation observed in the evolved AAO from S. cerevisiae underpinned this effect, since when the mutant was produced in the glycosylation-deficient S. cerevisiae strain Δkre2, its kinetic parameters and thermostability were comparable to its poorly glycosylated P. pastoris recombinant counterpart.
Sensing-Transmission Edifice Using Bayesian Nonparametric Traffic Clustering in Cognitive Radio Networks (2014)

In cognitive radio networks, the main objective of spectrum sensing is to exploit spectrum holes left by the primary users (PUs). Different PUs' traffic patterns might provide different opportunities for second user (SU) spectrum access. In this paper, we identify the PUs' traffic patterns and then maximize SU transmission accordingly. First a theoretical framework is developed to cluster PU traffic patterns based on a Bayesian nonparametric inference model, in which the number of traffic types is unknown. Second, in order to exploit the spectrum holes, we study a sensing-transmission structure to optimize the SU transmission strategy. Specifically, we exploit the short and long transmission opportunities based on the PU traffic pattern and channel idle time distribution. Finally, we propose a threshold-based sensing-transmission method that optimizes the SU utility, while protecting PU transmissions. Both sensing and transmission errors are considered for perfect sensing with/without acknowledgement-based transmission and imperfect sensing, respectively. From the simulation results, we show that the proposed technique outperforms the nonparametric mean shift clustering algorithm. Furthermore, we utilize these clustering results to optimize the SU's transmission strategy with perfect and imperfect sensing. We compare our proposed technique with the probabilistic sensing-transmission structure and show the performance gain in terms of throughput.
BREEDING FOR A LEBANESE TYPE OF TOMATO WITH COMBINED RESISTANCE TO TOMATO YELLOW LEAF CURL VIRUS, FUSARIUM AND VERTICILLIUM WILTS USING MARKER ASSISTED SELECTION TOOLS (2009)

ISHS II International Symposium on Tomato Diseases BREEDING FOR A LEBANESE TYPE OF TOMATO WITH COMBINED RESISTANCE TO TOMATO YELLOW LEAF CURL VIRUS, FUSARIUM AND VERTICILLIUM WILTS USING MARKER ASSISTED SELECTION TOOLS
Space environment durability of beta cloth in LDEF thermal blankets (1993)

Beta cloth performance for use on long-term space vehicles such as Space Station Freedom (S.S. Freedom) requires resistance to the degrading effects of the space environment. The major issues are retention of thermal insulating properties through maintaining optical properties, preserving mechanical integrity, and generating minimal particulates for contamination-sensitive spacecraft surfaces and payloads. The longest in-flight test of beta cloth's durability was on the Long Duration Exposure Facility (LDEF), where it was exposed to the space environment for 68 months. The LDEF contained 57 experiments which further defined the space environment and its effects on spacecraft materials. It was deployed into low-Earth orbit (LEO) in Apr. 1984 and retrieved Jan. 1990 by the space shuttle. Among the 10,000 plus material constituents and samples onboard were thermal control blankets of multilayer insulation with a beta cloth outer cover and Velcro attachments. These blankets were exposed to hard vacuum, thermal cycling, charged particles, meteoroid/debris impacts, ultraviolet (UV) radiation, and atomic oxygen (AO). Of these space environmental exposure elements, AO appears to have had the greatest effect on the beta cloth. The beta cloth analyzed in this report came from the MSFC Experiment S1005 (Transverse Flat-Plate Heat Pipe) tray oriented approximately 22 deg from the leading edge vector of the LDEF satellite. The location of the tray on LDEF and the placement of the beta cloth thermal blankets are shown. The specific space environment exposure conditions for this material are listed.
ChemInform Abstract: A New Approach to 1‐Alkyl‐1,3‐dihydro‐2H‐benzimidazol‐2‐ones. (1985)

Abstract Durch Reaktion der Nitroaniline (Ia) und (Ib) mit dem Ester (II) lassen sich die N‐Ethoxycarbonylverbindungen (IIIa) und (IIIb) synthetisieren.
SU‐GG‐I‐35: Geometric Accuracy of High Contrast Region Visualization On 4D X‐Ray CT Imaging Using Sinogram Binning (2008)

Purpose: To assess geometric errors in delineating high‐contrast structures from 4DCT‐acquired images undergoing simulated motion of various amplitudes. The broader goal is to formulate margin‐design guidelines that account for imperfections in 4D target imaging for a range of tumor sizes and motion amplitudes. Method and Materials: Three spherical objects with different diameters were placed on a moving platform adjusted to provide sinusoidal, one‐dimensional motions of various excursions (range: 0.5–4 cm) along the longitudinal axis of a Philips Brilliance scanner. Repeated scans were performed for three pitch values (0.15, 0.11, 0.075). Sinogram data were sorted into 10 different breathing phase bins. In addition, time‐averaged and maximum intensity projection (MIP) image sets were reconstructed. Data analysis included qualitative inspection of the shape of scanned objects, comparisons of contoured volumes for the static and moving targets, and centroid motion assessment. Results: The accuracy of reconstructed objects generally improves with decreasing amplitude and pitch. For large excursions and phases intermediate between exhale and inhale, large deviations from the spherical shape are observed; amplitude and volume deviations are as large as 10 mm and 30%. The observed centroid excursion is always less than the actual bin midpoint excursion. Smaller pitch does not always guarantee better results. The MIP centroid lines up closely with the centroid from time‐averaged datasets, but its actual position is underestimated by 3–4 mm as well. There is a tendency for deviations to be larger for datasets reconstructed during inhalation. Conclusion: The accuracy of 4D‐acquired datasets depends on motion characteristics and protocol acquisition parameters. The evaluation of the associated uncertainties is necessary for a more accurate margin design during treatment planning when either one or multiple 4D‐derived datasets are used for treatment planning. More studies are required to investigate the clinical significance of such errors. Supported in part by NIH P01 CA116602.
Replication in Simian Cells of Defective Viruses in an SV40-Adenovirus “Hybrid” Population (1966)

Butel, Janet S. (Baylor University College of Medicine, Houston, Tex.), and Fred Rapp. Replication in simian cells of defective viruses in an SV40-adenovirus "hybrid" population. J. Bacteriol. 91:278-284. 1966.-An SV40-adenovirus type 7 "hybrid" virus population, previously shown to contain two viruses capable of complementation in green monkey kidney (GMK) cells, has a growth cycle in GMK cells similar to that of adenovirus type 7 in the presence of SV40. Extending previous preliminary results, the addition of adenovirus types 2, 7, or 12 to monolayers of GMK cells enhanced plaque formation by the SV40-adenovirus hybrid by as much as 200-fold. The terminal enhanced plaques, initiated by the hybrid in the presence of helper adenovirus, were found to contain progeny which could induce the synthesis of SV40 tumor antigen but which were coated with the protein of the helper adenovirus, type 2, 7, or 12, respectively. The particle carrying the SV40 tumor antigen determinant, named PARA, is defective in that it cannot direct the synthesis of capsid protein; information for the coat for PARA is supplied by the adenovirus. One-step growth curves of the hybrid virus population in monkey cells revealed that synthesis of both types of particles, adenovirus and PARA, proceeds at a similar rate, with a latent period of 16 to 20 hr being followed by an exponential increase in titer during the following 20 hr. Maximal titers for both particles were obtained 48 hr after inoculation of the cultures. Neither the PARA nor the adenovirus component replicated in GMK cells in the absence of the other.
Bacteriological measures for the detection of cases of pulmonary tuberculosis. (1971)

There is a need for more detailed information on the relative merits of the culture and direct sputum smear examination methods, separately and in various combinations, using one or more sputum specimens. The efficiency and relative cost of different bacteriological measures for the detection of cases of pulmonary tuberculosis, in the conditions of the Singapore tuberculosis control programme, are demonstrated. The findings provide guidance for deciding how, and in what order, these bacteriological measures should be used, and may assist planners and executives of national tuberculosis control programmes in the rational commissioning of laboratory facilities that already exist or are to be established.
Automated capillary GC determination of local anaesthetics in plasma samples with supported liquid membranes for sample preparation (1998)

An on-line automatic system has been developed for the determination of local anaesthetics in untreated blood plasma samples. It utilizes supported liquid membrane extraction for initial sample preparation, a solid phase column for phase switching, and a capillary gas chromatographic final analysis. The extraction procedure is very selective, as no other compounds than the analytes are observed in the resulting chromatograms at low nanogram-per-milliliter concentration levels. The detection limits are about 1 ng/mL, and the precision is around 5%. The system is fully automated and permits the analysis of ca. 50 samples per day. © 1998 John Wiley & Sons, Inc. J Micro Sep 10: 107–113, 1998
Domain observation on magnetoresistive sensor elements (1996)

We investigate the domain behavior of different magnetoresistance sensor elements to optimize a sensor shape for high sensitivity applications. Some of the encountered remanent domain patterns are analyzed using a novel quantitative magnetooptic observation technique. The center coercivity field and the saturation field of the elements were measured as a clue for stability and sensitivity of the sensor element.
Lecture Vdeo Indexing Using Boosted Margin Maximizing Neural Networks (2017)

This paper presents a novel approach for lecture video indexing using a boosted deep convolutional neural network system. The indexing is performed by matching high quality slide images, for which text is either known or extracted, to lower resolution video frames with possible noise, perspective distortion, and occlusions. We propose a deep neural network integrated with a boosting framework composed of two sub-networks targeting feature extraction and similarity determination to perform the matching. The trained network is given as input a pair of slide image and a candidate video frame image and produces the similarity between them. A boosting framework is integrated into our proposed network during the training process. Experimental results show that the proposed approach is much more capable of handling occlusion, spatial transformations, and other types of noises when compared with known approaches.