gebhart/patrepeval huggingface dataset:
Cutaneous late‐phase response in food‐allergic children and adolescents with atopic dermatitis (1993)

Food hypersensitivities contribute to disease exacerbation in a sub-group of children with atopic dermatitis (AD). It has been shown that only selected foods are capable of causing clinical reactions when ingested, whereas other foods, to which the patient is equally sensitive by skin-prick testing, may be tolerated. The purpose of this study was to examine the cutaneous late-phase response (LPR) to food antigens in food-allergic patients with AD and to determine if the skin reacted differently to 'relevant foods' (foods eliciting positive skin-prick tests and positive oral challenges) than to 'non-relevant foods' (foods eliciting positive skin tests but negative oral challenges). Using blister chambers adfixed to the skin, six children with AD were challenged epicutaneously with foods to which they had previously been shown to be sensitive. Histamine and PGD2 were measured hourly for 10-12 hr in parallel with quantitation of the cellular traffic. There appeared to be no difference in any of the measured parameters between relevant foods and non-relevant foods, and the patterns of the LPR cells and mediators were similar to those previously described with aero-allergens in patients with respiratory allergy. Histamine rose to 13.0 +/- 24 ng/ml (P < 0.005) during the first hours, declined to < 1 ng/ml by the fifth hour, and then rose a second time to 6.72 +/- 3.4 ng/ml (P < 0.05) during the 12th hour. PGD2 rose to an average of 312 pg/ml (P < 0.05) during the first 3 hr followed by a decline to baseline.(ABSTRACT TRUNCATED AT 250 WORDS)
Novel Multiplex PCR Assay for Simultaneous Identification of Community-Associated Methicillin-Resistant Staphylococcus aureus Strains USA300 and USA400 and Detection of mecA and Panton-Valentine Leukocidin Genes, with Discrimination of Staphylococcus aureus from Coagulase-Negative Staphylococci (2007)

We developed a novel multiplex PCR assay for rapid identification and discrimination of the USA300 and USA400 strains and concomitant detection of Panton-Valentine leukocidin genes, with simultaneous discrimination of methicillin-resistant Staphylococcus aureus strains from methicillin-susceptible S. aureus strains, S. aureus strains from coagulase-negative staphylococci, and staphylococci from other bacteria.
Evaluating the Magnitude and Duration of Cold Load Pick-up on Residential Distribution FeedersUsing Multi-State Load Models (2015)

The increased level of demand that is associated with the restoration of service after an outage, Cold Load Pick-Up (CLPU), can be significantly higher than pre-outage levels, even exceeding the normal distribution feeder peak demand. These high levels of demand can delay restoration efforts and in extreme cases damage equipment. The negative impacts of CLPU can be mitigated with strategies that restore the feeder in sections, minimizing the load current. The challenge for utilities is to manage the current level on critical equipment while minimizing the time to restore service to all customers. Accurately modeling CLPU events is the first step in developing improved restoration strategies that minimize restoration times. This paper presents a new method for evaluating the magnitude of the CLPU peak, and its duration, using multi-state load models. The use of multi-state load models allows for a more accurate representation of the end-use loads that are present on residential distribution feeders.
The use of a [4 + 2] cycloaddition reaction for the preparation of a series of ‘tethered’ Ru(ii)–diamine and aminoalcohol complexes (2007)

A series of catalysts have been prepared for use in the asymmetric transfer hydrogenation of ketones. The complexes were prepared using a [4 + 2] cycloaddition reaction at a key step in the reaction sequence. This provides a means for the synthesis of catalysts with modifications at specific sites.
Aspirin Use and All-Cause Mortality Among Patients Being Evaluated for Known or Suspected Coronary Artery Disease (2001)

Aspirin use among patients undergoing stress echocardiography was independently associated with reduced long-term all-cause mortality, particularly among older patients, those with known coronary artery disease, and those with impaired exercise capacity.
Purity Assessment of Single-Wall Carbon Nanotubes, Using Optical Absorption Spectroscopy (2005)

A demand currently exists for a method of assessing the purity of single-wall carbon nanotubes (SWNTs), which will allow for meaningful material comparisons. An established metric and protocol will enable accurate and reproducible purity claims to be substantiated. In the present work, the ability to accurately quantify the mass fraction of SWNTs in the carbonaceous portion of a given sample is demonstrated, using optical absorption spectroscopy on both laser and arc discharge-generated SWNT-N,N-dimethylacetamide (DMA) dispersions. Verification of purity assessment protocols is based upon constructed sample sets comprising designed mass fractions of purified SWNTs and representative carbonaceous synthesis byproducts. Application of a previously reported method based on a ratio of the areal absorbance from linear subtractions of the second interband electronic transitions of semiconducting SWNTs ((S)E(22)) has shown a severe overestimation of SWNT purity (average error >24%). Instead, the development of a nonlinear pi-plasmon model, which considers overlap of electronic transitions and peak broadening, has dramatically improved the purity assessment accuracy (average error <7%), derived from a strong correlation to the constructed sample sets. This approach has enabled corroboration of rapid assessment procedures, such as absorbance peak maxima ratio and Beer's law analysis, directed at purification monitoring and synthesis sample screening. Specifically, a simple protocol for purity assessment of laser and arc-discharge SWNTs has been established that can be extended to other synthetic types (i.e. CVD, HiPco, etc.) and diameter distributions.
Aluminum Salen Complexes and Tetrabutylammonium Salts:  A Binary Catalytic System for Production of Polycarbonates from CO2 and Cyclohexene Oxide (2005)

A series of complexes of the form (salen)AlZ, where H2salen = N,N'-bis(salicylidene)-1,2-phenylenediimine and various other salen derivatives and Z = Et or Cl, have been synthesized. Several of these complexes have been characterized by X-ray crystallography. An investigation of the utilization of these aluminum derivatives along with both ionic and neutral bases as cocatalysts for the copolymerization of carbon dioxide and cyclohexene oxide has been conducted. By studying the reactivity of these complexes for this process as substituents on the diimine backbone and phenolate rings are altered, we have observed that aluminum prefers electron-withdrawing groups on the salen ligands, thereby producing an electrophilic metal center to be most active toward production of polycarbonates from CO2 and cyclohexene oxide. For example, the complex derived from H2salen = N,N'-bis(3,5-di-tert-butylsalicylidene)-1,2-ethylenediimine is essentially inactive when compared to the analogous derivative containing nitro substituents in the 3-positions of the phenolate groups. This is to be contrasted with the catalytic activity observed for the (salen)CrX systems, where electron-donating salen ligands greatly enhanced the reactivity of these complexes for the coupling of CO2 and epoxides. While (salen)AlZ complexes are capable of producing poly(cyclohexene oxide) carbonate with low amounts of polyether linkage along with small quantities of cyclic carbonate byproducts, their reactivities, covering a turnover frequency range of 5.2-35.4 mol of epoxide consumed/(mol of Al x h), are greatly reduced when compared to their (salen)CrX analogues under identical reaction conditions.
Kinase-Dead BRAF and Oncogenic RAS Cooperate to Drive Tumor Progression through CRAF (2010)

We describe a mechanism of tumorigenesis mediated by kinase-dead BRAF in the presence of oncogenic RAS. We show that drugs that selectively inhibit BRAF drive RAS-dependent BRAF binding to CRAF, CRAF activation, and MEK-ERK signaling. This does not occur when oncogenic BRAF is inhibited, demonstrating that BRAF inhibition per se does not drive pathway activation; it only occurs when BRAF is inhibited in the presence of oncogenic RAS. Kinase-dead BRAF mimics the effects of the BRAF-selective drugs and kinase-dead Braf and oncogenic Ras cooperate to induce melanoma in mice. Our data reveal another paradigm of BRAF-mediated signaling that promotes tumor progression. They highlight the importance of understanding pathway signaling in clinical practice and of genotyping tumors prior to administering BRAF-selective drugs, to identify patients who are likely to respond and also to identify patients who may experience adverse effects.
Seed-specific expression of the isopentenyl transferase gene ( ipt ) in transgenic tobacco (1998)

The Agrobacterium tumefaciens gene encoding isopentenyl transferase ( ipt ), a cytokinin biosynthetic gene, was fused to a promoter from a seed-specific gene, vicilin, and introduced into tobacco cells. Intact fertile plants were generated. The expression of the vicilin-ipt gene was shown to be confined to seed and resulted in enhanced levels of cytokinins in the developing seeds and increased seed protein content. Using a simplified quantification method, a significant increase in the levels of endogenous cytokinins was recorded at 16–21 days after flowering. The growth of the transgenic plants and the development of the seeds appeared to be normal.
Transgenic mice bearing the human c-myc gene activated by an immunoglobulin enhancer: a pre-B-cell lymphoma model. (1988)

Transgenic mice carrying a fusion gene in which the mouse immunoglobulin enhancer has been inserted into an otherwise normal human c-myc gene develop a narrow spectrum of pre-B-cell lymphomas. Tumor occurrence is correlated with expression of the transgene in organs in which large numbers of pre-B cells predominate. These tumors, which arise stochastically, are virtually all lymphoblastic lymphomas of the pre-B-cell type. Evidently the isolated enhancer targets oncogene expression and tumorigenesis to the early B-cell population in preference to more mature B-cell populations. The transgene also confers enhanced in vitro growth properties on nontransformed pre-B cells as observed in bone marrow cultures derived from transgenic animals. These cultured cells represent a population in which the activating function of c-myc can be uncoupled from secondary oncogenic events occurring in vivo.
Genetics of staphylococcal enterotoxin B in methicillin-resistant isolates of Staphylococcus aureus (1979)

Biophysical and genetic analysis of staphylococcal enterotoxin B (SEB) synthesis in 16 methicillin-resistant (Mecr) Staphylococcus aureus isolates demonstrated that the toxin gene (entB) can occupy either a plasmid or chromosomal locus. Biophysical analysis of the plasmid deoxyribonucleic acid content of these strains by agarose gel electrophoresis revealed the presence of a 1.15-megadalton plasmid in six isolates that appears to contain the entB gene. Genetic manipulation of SEB synthesis by transduction and elimination procedures demonstrated that this plasmid is critical for enterotoxigenesis. Nevertheless, the majority of the Mecr SEB+ isolates (62.5%) analyzed in this investigation were found to lack the 1.15-megadalton plasmid. In at least two of these strains (COL and 57-dk), transduction and elimination procedures showed that entB was chromosomal. Genetic studies involving strains harboring either a plasmid or chromosomal entB gene demonstrated that toxin synthesis was coeliminated with mec. However, analysis of the entB and mec loci by transformation or transduction showed that the genes are not closely linked. On the other hand, transduction of entB, regardless of the donor, was observed when both mec and the Tcr plasmid were jointly cotransduced. This finding suggests that, during transduction, a transient association between entB, mec, and the Tcr plasmid may exist.
Engineering an APRIL-specific B Cell Maturation Antigen (2004)

B cell maturation antigen (BCMA) is a tumor necrosis factor receptor family member whose physiological role remains unclear. BCMA has been implicated as a receptor for both a proliferation-inducing ligand (APRIL) and B cell-activating factor (BAFF), tumor necrosis factor ligands that bind to multiple tumor necrosis factor receptor and have been reported to play a role in autoimmune disease and cancer. The results presented herein provide a dual perspective analysis of BCMA binding to both APRIL and BAFF. First, we characterized the binding affinity of monomeric BCMA for its ligands; BAFF binding affinity (IC50 = 8 +/- 5 microm) is about 1000-fold reduced compared with the high affinity interaction of APRIL (IC50 = 11 +/- 3 nm). Second, shotgun alanine scanning of BCMA was used to map critical residues for either APRIL or BAFF binding. In addition to a previously described "DXL" motif (Gordon, N. C., Pan, B., Hymowitz, S. G., Yin, J., Kelley, R. F., Cochran, A. G., Yan, M., Dixit, V. M., Fairbrother, W. J., and Starovasnik, M. A. (2003) Biochemistry 42, 5977-5983), the alanine scanning results predicted four amino acid positions in BCMA (Tyr13, Ile22, Gln25, and Arg27) that could impart ligand specificity. Substitution of Tyr13 was tolerated for BAFF binding but not APRIL binding. Arg27 was required for high affinity binding to APRIL, whereas substitutions of this residue had minimal effect on affinity for BAFF. Further phage display experiments suggested the single mutations of I22K, Q25D, and R27Y as providing the greatest difference in APRIL versus BAFF binding affinity. Incorporation of the Q25D and R27Y substitutions into BCMA produced a dual specificity variant, since it has comparable binding affinity for both APRIL and BAFF, IC50 = 350 and 700 nm, respectively. Binding of the I22K mutant of monomeric BCMA to BAFF was undetectable (IC50 > 100 microm), but affinity for binding to APRIL was similar to wild-type BCMA. Based on these results, a BCMA-Fc fusion with the single I22K mutation was produced that binds APRIL, IC50 = 12 nm, and has no measurable affinity for BAFF. These results suggest that APRIL is the preferred ligand for BCMA and show that specificity can be further modified through amino acid substitutions.
Graph-Based Analysis and Optimization of Contention Resolution Diversity Slotted ALOHA (2010)

Contention resolution diversity slotted ALOHA (CRDSA) is a simple but effective improvement of slotted ALOHA. CRDSA relies on MAC bursts repetition and on interference cancellation (IC), achieving a peak throughput T ≅ 0.55, whereas for slotted ALOHA T ≅ 0.37. In this paper we show that the IC process of CRDSA can be conveniently described by a bipartite graph, establishing a bridge between the IC process and the iterative erasure decoding of graph-based codes. Exploiting this analogy, we show how a high throughput can be achieved by selecting variable burst repetition rates according to given probability distributions, leading to irregular graphs. A framework for the probability distribution optimization is provided. Based on that, we propose a novel scheme, named irregular repetition slotted ALOHA, that can achieve a throughput T ≅ 0.97 for large frames and near to T ≅ 0.8 in practical implementations, resulting in a gain of ~ 45% w.r.t. CRDSA. An analysis of the normalized efficiency is introduced, allowing performance comparisons under the constraint of equal average transmission power. Simulation results, including an IC mechanism described in the paper, substantiate the validity of the analysis and confirm the high efficiency of the proposed approach down to a signal-to-noise ratio as a low as E <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">b</sub> /N <sub xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">0</sub> =2 dB.
Kromoscopic analysis: a possible alternative to spectroscopic analysis for noninvasive measurement of analytes in vivo (1994)

Light that penetrates scattering media shows nonlinearities that mask the broad and shallow perturbations made by trace analytes on the background illuminant spectrum. Narrow-band spectroscopic decomposition and deconvolution of such weak bands is a formidable analytical task that pushes the fundamentally linear spectroscopic method beyond practical limits. Kromoscopy is a high-dimensional analog of human color perception; it has broad-band spectrally overlapping detectors similar to those of the visual system, but in the infrared. Analyte bands are integrated fully in two or more detectors with different relative weightings. As in color vision, the analyte information is coded in the direct correlations between detector signals, which individually have higher signal-to-noise ratios than their spectroscopic counterparts. Our Kromoscopic instrument responds directly to glucose in aqueous solution, is not affected by temperature disturbances, and is fast enough to measure physiologically induced Kromoscopic changes in the arterial pulse waveform with high precision.
Towards an integrated view of Wnt signaling in development (2009)

Wnt signaling is crucial for embryonic development in all animal species studied to date. The interaction between Wnt proteins and cell surface receptors can result in a variety of intracellular responses. A key remaining question is how these specific responses take shape in the context of a complex, multicellular organism. Recent studies suggest that we have to revise some of our most basic ideas about Wnt signal transduction. Rather than thinking about Wnt signaling in terms of distinct, linear, cellular signaling pathways, we propose a novel view that considers the integration of multiple, often simultaneous, inputs at the level of both Wnt-receptor binding and the downstream, intracellular response.
Alzheimer-like paired helical filaments and antiparallel dimers formed from microtubule-associated protein tau in vitro. (1992)

Recent evidence from several laboratories shows that the paired helical filaments of Alzheimer's disease brains consist mainly of the protein tau in an abnormally phosphorylated form, but the mode of assembly is not understood. Here we use EM to study several constructs derived from human brain tau and expressed in Escherichia coli. All constructs or tau isoforms are rodlike molecules with a high tendency to dimerize in an antiparallel fashion, as shown by antibody labeling and chemical crosslinking. The length of the rods is largely determined by the region of internal repeats that is also responsible for microtubule binding. One unit length of the repeat domain (three or four repeats) is around 22-25 nm, comparable to the cross-section of Alzheimer PHF cores. Constructs corresponding roughly to the repeat region of tau can form synthetic paired helical filaments resembling those from Alzheimer brain tissue. A similar self-assembly occurs with the chemically cross-linked dimers. In both cases there is no need for phosphorylation of the protein.
Functional fusions of T4 lysozyme in the third intracellular loop of a G protein-coupled receptor identified by a random screening approach in yeast (2012)

The insertion of a stable soluble protein into loops of transmembrane proteins has proved to be a successful approach for enhancing their stabilities and crystallization, and may also be useful in contexts where the inserted proteins can modulate or report on the activities of membrane proteins. While the use of T4 lysozyme to replace portions of the third intracellular loops of G proteincoupled receptors (GPCRs) has allowed determination of the structures of members of this important class of receptors, the creation of such fusion proteins generally leads to loss of signaling function of the resulting fusion protein, since the third intracellular loops of GPCRs play critical roles in their interactions with G proteins. We describe here a random screening approach allowing insertion of T4 lysozyme into diverse positions in the third loop of the yeast a-pheromone receptor, a GPCR encoded by the yeast STE2 gene. Insertions were accompanied by varying extents of deletion or duplication of the loop. A set of phenotypic screens allow detection of potentially rare variant receptors that are expressed, bind to agonist and are capable of signal transduction via activation of the cognate G protein. A large fraction of screened full-length receptor variants containing at least partial duplications of the loop on either side of the inserted T4 lysozyme retain the ability to activate the downstream signaling pathway in response to binding of ligand. However, we were unable to identify any receptors with truncated C-termini that retain significant signaling function in the presence of inserted T4 lysozyme. Our results establish the feasibility of creating functional receptors containing insertions of T4 lysozyme in their third intracellular loops.
Monoclonal antibodies to kidney and tumor-associated surface antigens of human renal cell carcinoma. (1986)

Three IgG1 monoclonal antibodies derived from BALB/c mice immunized with the Caki-1 human renal cell carcinoma (RCC) line react with antigens present in most human RCCs but restricted in their expression in normal adult tissues. Antibody DAL-K20 reacted with five of six RCCs and the lining epithelium of normal proximal and distal convoluted tubules. Antibody DAL-K29 reacted with eight of nine RCCs, with glomeruli, where it outlined the capillaries, and more weakly with prostatic glandular epithelium and the basal layer of the epidermis. K29 precipitated molecules with molecular weights of 118,000 and 150,000 from extracts of surface-labeled Caki-1 cells. Antibody DAL-K45 reacted with four of six RCCs but not with any normal adult tissue including kidney. It precipitated Mr 177,000 and 150,000 antigens. The three antibodies showed distinct patterns of reactivity with human tumor cell lines.
A Comparative Analysis and Evaluation of Neka River Basin Deforested Land from 1977-2006 using MSS, TM and ETM Satellite Images (2013)

The main objective of this study is to find out the loss of forest area through analyzing it in different periods. In general, deforestation can be regarded as one of the most important elements in LULC and the scenario of global changes is taking place around the world. Therefore, it is worth assessing its trend and the rate at which it is taking place now. These changes will play a significant role in bringing about some changes in regional climate and accordingly on biodiversity. The loss of forest in Iran is going on since 1960 onwards in the Neka river Basin. The estimation of forest loss was not reported to be done by using Satellite data. The changes occurring in forest cover were reported by a series of four satellite images in different time intervals by using Remote Sensing (RS) and GIS such as Land satMSS of 1977, Land satTM of1987, ETM 2001 and ETM+ 2006. The forest covers were analyzed and maps from four temporal satellite datasets were prepared. Based on 1977, 1987, 2001 and 2006 satellite data interpretation, the forest cover was converted to geospatial database. According to the results obtained from these images, there was a decrease in forest area (7096.63), productive forest area, as well as degraded forest area. However, the total forest area showed a decrease in the first period (1977-1987) although an increase was reported again during the second period (1987-2001) to 2418.82 hectares (3.5% of the study area), this trend continued even between 2001-2006 and the mixed forest cover increased by856.08 hectares (1.31%). This increase was due to few hectares of mixed forest area was converted into manmade forest.