gebhart/patrepeval huggingface dataset:
Avidity as a Determinant of the Protective Efficacy of Human Antibodies to Pneumococcal Capsular Polysaccharides (1999)

Antibodies reactive with capsular polysaccharides are considered the principal mediators of immunity against invasive diseases caused by Streptococcus pneumoniae. In this study, we tested the hypothesis that anti-pneumococcal capsular polysaccharide (PPS) antibody avidity can influence protective efficacy. We measured the avidities of individual adult postvaccination immunoglobulin G2 (IgG2) antibodies to PPS serotypes 6B and 23F and examined the relationship between avidity and opsonophagocytic and mouse-protective activities. The avidities of PPS 6B- and PPS 23F-specific IgG2 antibodies ranged from 6 to 31 nM-1 and from 3 to 20 nM-1, respectively. We observed an inverse correlation between the magnitude of avidity and the amount of antibody required to protect mice against lethal bacteremia caused by serotype 6B pneumococci. Similarly, higher-avidity antibodies were more effective than lower-avidity antibodies in vitro in mediating complement-dependent opsonophagocytosis of both 6B and 23F pneumococci. These data suggest that in adults, PPS antibodies are sufficiently polymorphic to possess biologically significant variations in avidity. We conclude that avidity functions as an important determinant of anticapsular antibody protective efficacy against pneumococci.
ChemInform Abstract: Kotalanol, a Potent α‐Glucosidase Inhibitor with Thiosugar Sulfonium Sulfate Structure, from Antidiabetic Ayurvedic Medicine Salacia reticulata. (1999)

Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a “Full Text” option. The original article is trackable via the “References” option.
Path profile guided partial redundancy elimination using speculation (2002)

While programs contain a large number of paths, a very small fraction of these paths are typically exercised during program execution. Thus, optimization algorithms should be designed to trade off the performance of less frequently executed paths in favor of more frequently executed paths. However, traditional formulations to code optimizations are incapable of performing such a trade-off. The authors present a path profile guided partial redundancy elimination algorithm that uses speculation to enable the removal of redundancy along more frequently executed paths at the expense of introducing additional expression evaluations along less frequently executed paths. They describe cost-benefit data flow analysis that uses path profiling information to determine the profitability of using speculation. The cost of enabling speculation of an expression at a conditional is determined by identifying paths along which an additional evaluation of the expression is introduced. The benefit of enabling speculation is determined by identifying paths along which additional redundancy elimination is enabled by speculation. The results of this analysis are incorporated in a speculative expression hoisting framework for partial redundancy elimination.
Validation of the Image of Science and Scientists Scale (1979)

The Image of Science and Scientists Scale was developed to assess high school students' attitudes toward science as a field of study. Reliability and three types of validity evidence are reported for the scale.
EPR spectrometer for clinical applications (2005)

This article describes an EPR spectrometer specifically designed and constructed for EPR spectroscopy in humans. The spectrometer is based on a permanent magnet, suitable for measurements at 1200 MHz. The magnet has a full 50 cm gap between the poles, which facilitates accurate and comfortable placement of the subject for the EPR measurement at any location on the human body. The bridge includes features to facilitate clinical operations, including an indicator for phasing of the reference arm and a 2 level RF amplifier. Resonators with holders for each type and site of measurement have been developed that comfortably position the resonator and the patient and prevent artifacts due to motion. The initial applications for which the spectrometer has been designed are for oximetry using loops on the surface, oximetry using implanted resonators for measuring deep sites, and measurements in the teeth for determination of exposures to clinically significant doses of ionizing radiation.
Numerical recipes example diskette (Pascal) (1989)

This revised example diskette for the Macintosh contains the test programs found in the revised Pascal example book (0521 376750). As with the diskette for the main text, the programs are supplied in source code for manipulation and incorporation by users into their own programs. (Requires the corresponding Numerical Recipes diskette to run).
Iron-Catalyzed 1,4-Addition of α-Olefins to Dienes (2008)

A new intermolecular, stereo- and regioselective iron-catalyzed 1,4-addition of alpha-olefins to 1,3-dienes using as low as 1 mol % of an iminopyridine-ferrous chloride complex was developed. Importantly, both double bonds of the linear 1,4-diene addition products are obtained with absolute stereocontrol.
Generating Interactive Worlds with Text (2020)

Procedurally generating cohesive and interesting game environments is challenging and time-consuming. In order for the relationships between the game elements to be natural, common-sense has to be encoded into arrangement of the elements. In this work, we investigate a machine learning approach for world creation using content from the multi-player text adventure game environment LIGHT (Urbanek et al. 2019). We introduce neural network based models to compositionally arrange locations, characters, and objects into a coherent whole. In addition to creating worlds based on existing elements, our models can generate new game content. Humans can also leverage our models to interactively aid in worldbuilding. We show that the game environments created with our approach are cohesive, diverse, and preferred by human evaluators compared to other machine learning based world construction algorithms.
Characterization of Trapped Lignin-Degrading Microbes in Tropical Forest Soil (2011)

Lignin is often the most difficult portion of plant biomass to degrade, with fungi generally thought to dominate during late stage decomposition. Lignin in feedstock plant material represents a barrier to more efficient plant biomass conversion and can also hinder enzymatic access to cellulose, which is critical for biofuels production. Tropical rain forest soils in Puerto Rico are characterized by frequent anoxic conditions and fluctuating redox, suggesting the presence of lignin-degrading organisms and mechanisms that are different from known fungal decomposers and oxygen-dependent enzyme activities. We explored microbial lignin-degraders by burying bio-traps containing lignin-amended and unamended biosep beads in the soil for 1, 4, 13 and 30 weeks. At each time point, phenol oxidase and peroxidase enzyme activity was found to be elevated in the lignin-amended versus the unamended beads, while cellulolytic enzyme activities were significantly depressed in lignin-amended beads. Quantitative PCR of bacterial communities showed more bacterial colonization in the lignin-amended compared to the unamended beads after one and four weeks, suggesting that the lignin supported increased bacterial abundance. The microbial community was analyzed by small subunit 16S ribosomal RNA genes using microarray (PhyloChip) and by high-throughput amplicon pyrosequencing based on universal primers targeting bacterial, archaeal, and eukaryotic communities. Community trends were significantly affected by time and the presence of lignin on the beads. Lignin-amended beads have higher relative abundances of representatives from the phyla Actinobacteria, Firmicutes, Acidobacteria and Proteobacteria compared to unamended beads. This study suggests that in low and fluctuating redox soils, bacteria could play a role in anaerobic lignin decomposition.
G Protein–Coupled Receptor Sorting to Endosomes and Lysosomes (2007)

The heptahelical G protein-coupled receptors (GPCRs) belong to the largest family of cell surface signaling receptors encoded in the human genome. GPCRs signal to diverse extracellular stimuli and control a vast number of physiological responses, making this receptor class the target of nearly half the drugs currently in use. In addition to rapid desensitization, receptor trafficking is crucial for the temporal and spatial control of GPCR signaling. Sorting signals present in the intracytosolic domains of GPCRs regulate trafficking through the endosomal-lysosomal system. GPCR internalization is mediated by serine and threonine phosphorylation and arrestin binding. Short, linear peptide sequences including tyrosine- and dileucine-based motifs, and PDZ ligands that are recognized by distinct endocytic adaptor proteins also mediate internalization and endosomal sorting of GPCRs. We present new data from bioinformatic searches that reveal the presence of these types of sorting signals in the cytoplasmic tails of many known GPCRs. Several recent studies also indicate that the covalent modification of GPCRs with ubiquitin serves as a signal for internalization and lysosomal sorting, expanding the diversity of mechanisms that control trafficking of mammalian GPCRs.
Demonstration, of Insulin Resistance in Coronary Artery Disease Documented With Angiography (1996)

OBJECTIVE To evaluate the relation between insulin resistance and coronary atherosclerosis, insulin sensitivity in lean nondiabetic, normotensive subjects with and without obstructive coronary artery disease (CAD). The correlation between insulin resistance and degree of coronary stenosis was also investigated. RESEARCH DESIGN AND METHODS Four groups were studied: 1) nine subjects with normal glucose tolerance(NGT) without CAD, 2) 10 subjects with NGT with CAD, 3) nine subjects withimpaired glucose tolerance (IGT) without CAD, and 4) 10 subjects with IGT with CAD. Insulin sensitivity was determined by the steady-state plasma glucose (SSPG) method using Sandostatin. Coronary angiography was performed in all study subjects, and the severity of coronary artery atherosclerosis wasquantified in a modified Gensini score. RESULTS The SSPG (millimoles per liter) levels were significantly higher in the patients with CAD compared with control subjects (control vs. patient group: 4.8 ±0.5 vs. 7.9 ± 0.9 with NGT, P &lt; 0.05; 5.6 ± 0.5 vs. 11.1 ± 0.8 with IGT, P &lt; 0.001), indicating the presence of insulin resistance in patients with CAD. The coronary atherosclerosis score (CAS) was significantly and positively correlated with SSPG (r = 0.74, P &lt; 0.05) and 2-h insulin area (r = 0.78, P &lt; 0.01) in NGT subjects with CAD. On the other hand, the percentage fall of plasma free fatty acid (0–30 min) during an insulin sensitivity test was significantly decreased in the subjects with CAD and was inversely correlated with the CAS (r = −0.43, P &lt; 0.05), especially in NGT subjects with CAD. CONCLUSIONS These data suggest that in patients with CAD, insulin-mediated glucose metabolism is significantly impaired, and a significant correlation was noted between insulin resistance and severity of CAD. Therefore, the hyperinsulinemia often observed in patients with CAD is attributable to the compensatory mechanism of the β-cell to the inadequate action of insulin for glucose metabolism. Hyperinsulinemia in the presence of insulin resistance aggravates dyslipidemia and may stimulate the atheromatous process by an as-yet-unknown mechanism.
Direct Spectrophotometric Method for Measurement of Bilirubin in Newborns: Comparison with HPLC and an Automated Diazo Method (2002)

The measurement of serum total bilirubin is one of the most frequently performed tests in newborns (1)(2)(3). Direct spectrophotometry for the measurement of bilirubin in sera from newborns is a simple and rapid method that requires minimal sample for analysis (4). The direct spectrophotometric assay is based on the absorbance of bilirubin at 454 nm; by contrast, hemoglobin absorbs equally at both 454 and 528 nm. Subtraction of the absorbance at 528 nm from that at 454 nm eliminates the effect of hemolysis and yields a value that can be attributed primarily to bilirubin. Unfortunately, other pigments, such as carotenoids, also absorb at 454 nm, thus limiting this technique to neonates <2–3 weeks of age.

Direct spectrophotometric methods have been compared with diazo (Jendrassik–Grof-based) bilirubin methods (5)(6)(7)(8)(9), but sample hemolysis can increase or decrease the results obtained by the latter procedure, depending on the concentrations of hemoglobin and bilirubin in the sample (10)(11). Most such studies either do not describe the effect of sample hemolysis on the agreement between methods or report poorer agreement between methods or increased scatter around the regression line (6)(8)(9).

HPLC for measurement of serum bilirubin concentrations is labor-intensive and not practical for routine use; …
Block-Copolymer-Based Plasmonic Nanostructures (2009)

We report on the fabrication and optical characterization of dense and ordered arrays of metal nanoparticles. The metal arrays are produced by reducing metal salts in block copolymer (BCP) templates made by solvent annealing of poly(styrene-b-4-vinylpyridine) (PS-b-P4VP) or poly(styrene-b-ethylene oxide) (PS-b-PEO) diblock copolymer thin films in mixed solvents. The gold and gold/silver composite nanoparticle arrays show characteristic surface plasmon resonances in the visible wavelength range. The patterning can be applied over large areas onto various substrates. We demonstrate that these metal nanoparticle arrays on metal thin films interact with surface plasmon polaritons (SPPs) that propagate at the film/nanoparticle interface and, therefore, modify the dispersion relation of the SPPs.
Ethylene Butyl Acrylate Glycidyl Methacrylate Terpolymer as an Interfacial Agent for Isotactic Poly(propylene)/Wood Flour Composites (2006)

Abstract Summary: This paper presents the results of an experimental investigation concerning the use of an ethylene butyl acrylate and glycidyl methacrylate (EBAGMA) terpolymer as an interfacial agent for isotactic poly(propylene)/wood flour (iPP/WF) composites at various filler ratios (10, 20 and 30 wt.‐%). The effects of the EBAGMA terpolymer on the morphology, tensile properties, impact strength and water uptake of the iPP/WF composites were studied and the results were compared with those obtained with maleated poly(propylene) (MAPP) used as a compatibilizer. Initially, the mixing process was performed in a calendaring unit at 170 °C for pre‐homogenization of the filler in the matrix. Composites made out of these combinations were then ground and injected into a standard mold at 180 °C in the absence and the presence of compatibilizer. The results indicated that both EBAGMA terpolymer and MAPP improved the interactions between iPP and WF, and induced a better dispersion of wood particles in the polymer matrix, as revealed by scanning electron microscopy (SEM). Furthermore, tensile properties and impact strength were also increased. Another important effect was on the water absorption property, which was significantly lower for the samples with EBAGMA and MAPP. However, EBAGMA terpolymer produced better enhancement of the properties of the iPP/WF composites compared to the compatibilized samples with MAPP. SEM micrographs of the fracture surface of iPP/WF composites (70/30 wt.‐%): (a) without compatibilizer; (b) with 10 pph EBAGMA; (c) with 10 pph MAPP. Magnification was ×500. magnified image SEM micrographs of the fracture surface of iPP/WF composites (70/30 wt.‐%): (a) without compatibilizer; (b) with 10 pph EBAGMA; (c) with 10 pph MAPP. Magnification was ×500.
Low-loss, 2 km-long photonic crystal fiber with zero GVD in the near IR suitable for picosecond pulse propagation at the 800 nm band (2001)

Summary form only given. A 2 km-long hexagonal photonic crystal fiber with losses at 1550 and 850 nm of 3.2 and 7.1 dB/km, respectively, was successfully fabricated. The zero GVD wavelength was measured to be 810 nm, and picosecond optical pulses at 815 nm were successfully propagated through the fiber.
Cell Entry of the Aphthovirus Equine Rhinitis A Virus Is Dependent on Endosome Acidification (2010)

Equine rhinitis A virus (ERAV) is genetically closely related to foot-and-mouth disease virus (FMDV), and both are now classified within the genus Aphthovirus of the family Picornaviridae. For disease security reasons, FMDV can be handled only in high-containment facilities, but these constraints do not apply to ERAV, making it an attractive alternative for the study of aphthovirus biology. Here, we show, using immunofluorescence, pharmacological agents, and dominant negative inhibitors, that ERAV entry occurs (as for FMDV) via clathrin-mediated endocytosis and acidification of early endosomes. This validates the use of ERAV as a model system to study the mechanism of cell entry by FMDV.
ADA3: a gene, identified by resistance to GAL4-VP16, with properties similar to and different from those of ADA2. (1993)

We describe the isolation of a yeast gene, ADA3, mutations in which prevent the toxicity of GAL4-VP16 in vivo. Toxicity was previously proposed to be due to the trapping of general transcription factors required at RNA polymerase II promoters (S. L. Berger, B. Piña, N. Silverman, G. A. Marcus, J. Agapite, J. L. Regier, S. J. Triezenberg, and L. Guarente, Cell 70:251-265, 1992). trans activation by VP16 as well as the acidic activation domain of GCN4 is reduced in the mutant. Other activation domains, such as those of GAL4 and HAP4, are only slightly affected in the mutant. This spectrum is similar to that observed for mutants with lesions in ADA2, a gene proposed to encode a transcriptional adaptor. The ADA3 gene is not absolutely essential for cell growth, but gene disruption mutants grow slowly and are temperature sensitive. Strains doubly disrupted for ada2 and ada3 grow no more slowly than single mutants, providing further evidence that these genes function in the same pathway. Selection of initiation sites by the general transcriptional machinery in vitro is altered in the ada3 mutant, providing a clue that ADA3 could be a novel general transcription factor involved in the response to acidic activators.
Analysis of deletion of the integrated human papillomavirus 16 sequence in cervical cancer: A rapid multiplex polymerase chain reaction approach (1994)

A protocol for a rapid physical mapping of the integrated type 16 human papillomavirus (HPV16) sequences in biopsied and paraffin-embedded archival cervical cancer samples is described. The procedure involves the use of an anchor primer and a mixture of indicator primers in a multiplex polymerase chain reaction (PCR). A minimal conserved region of viral integration of 2,745 bp in length has been mapped between nucleotide (nt) 6102-941, containing the entire regulatory region and the E6 and E7 open reading frames (ORFs). A general deletion domain of 1,465 bp in the integrated viral genome has been defined between nt 1417-2881, covering most of the E1 ORF at the 3'-half and 60 bp at the 5' terminus of the E2 ORF. This common deleted sequence contains an ATPase active domain speculated to be associated with a DNA helicase function essential for the viral replication, and it also falls within the actively spliced E1-E2 segment of the primary RNA transcripts. Detection of the loss of the 3'-half of the E1 ORF would be an ideal marker for PCR-based rapid determination of HPV integration in cervical cancer cells.
A controllable piecewise linear-output circuit for CCD multiplexers (1985)

In certain applications, the single gain of the familiar reset-gate floating-diffusion output circuit limits the performance of a charge-coupled device (CCD) multiplexer used in a focal-plane array (FPA). Incorporation of an additional capacitor at the floating-diffusion node along with a switching MOSFET allows the output circuit to controllably switch from a high-gain to a low-gain state, thereby increasing the performance when detecting both large and small charge packets. This paper first describes such a circuit and then presents experimental results to verify its theory of operation. Discussion of a particular application is also given.
A Survey of Genome Editing Activity for 16 Cas12a Orthologs (2019)

The class 2 CRISPR-Cas endonuclease Cas12a (previously known as Cpf1) offers several advantages over Cas9, including the ability to process its own array and the requirement for just a single RNA guide. These attributes make Cas12a promising for many genome engineering applications. To further expand the suite of Cas12a tools available, we tested 16 Cas12a orthologs for activity in eukaryotic cells. Four of these new enzymes demonstrated targeted activity, one of which, from Moraxella bovoculi AAX11_00205 (Mb3Cas12a), exhibited robust indel formation. We also showed that Mb3Cas12a displays some tolerance for a shortened PAM (TTN versus the canonical Cas12a PAM TTTV). The addition of these enzymes to the genome editing toolbox will further expand the utility of this powerful technology.
Semantic Gateway as a Service Architecture for IoT Interoperability (2015)

The Internet of Things (IoT) is set to occupy a substantial component of future Internet. The IoT connects sensors and devices that record physical observations to applications and services of the Internet[1]. As a successor to technologies such as RFID and Wireless Sensor Networks (WSN), the IoT has stumbled into vertical silos of proprietary systems, providing little or no interoperability with similar systems. As the IoT represents future state of the Internet, an intelligent and scalable architecture is required to provide connectivity between these silos, enabling discovery of physical sensors and interpretation of messages between the things. This paper proposes a gateway and Semantic Web enabled IoT architecture to provide interoperability between systems, which utilizes established communication and data standards. The Semantic Gateway as Service (SGS) allows translation between messaging protocols such as XMPP, CoAP and MQTT via a multi-protocol proxy architecture. Utilization of broadly accepted specifications such as W3Cs Semantic Sensor Network (SSN) ontology for semantic annotations of sensor data provide semantic interoperability between messages and support semantic reasoning to obtain higher-level actionable knowledge from low-level sensor data.