gebhart/patrepeval huggingface dataset:
Identification of the human beta-actin enhancer and its binding factor. (1988)

An enhancer of the human beta-actin gene and a factor that specifically interacts with it were detected. A mobility shift assay showed that the factor bound to the 25-base-pair sequence (between +759 and +783 downstream from the cap site) with high specificity. This finding correlated with those of DNase I protection and exonuclease III digestion assays. This binding region of the beta-actin enhancer contained a hyphenated dyad symmetry and an enhancer core-like sequence. In vitro competition experiments indicated that the factor did not bind to the simian virus 40 enhancer core region.
An introduction to genetic algorithms for electromagnetics (1995)

This article is a tutorial on using genetic algorithms to optimize antenna and scattering patterns. Genetic algorithms are "global" numerical-optimization methods, patterned after the natural processes of genetic recombination and evolution. The algorithms encode each parameter into binary sequences, called a gene, and a set of genes is a chromosome. These chromosomes undergo natural selection, mating, and mutation, to arrive at the final optimal solution. After providing a detailed explanation of how a genetic algorithm works, and a listing of a MATLAB code, the article presents three examples. These examples demonstrate how to optimize antenna patterns and backscattering radar-cross-section patterns. Finally, additional details about algorithm design are given.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Evaluation of human conjunctival epithelium by a combination of brush cytology and flow cytometry: An approach to the quantitative technique (1997)

Cytology using the brush technique is readily available and is a rapid means of establishing a presumptive diagnosis of ocular surface changes. However, those techniques have some limitations when obtaining cells from certain localized areas particularly if using the Cytobrush-S. We have described here a new type of brush (Accellon-M), which can collect the local cells using its spherical tip, and evaluated them by comparing with Cytobrush-S. Furthermore, we differentiated epithelial cells from nonepithelial cells that were collected by brushing, and by a combination of brush cytology and flow cytometry using an anti-keratin antibody, AE-3, which reacts with all basic epithelial keratins. Accellon-M could collect the epithelial cells from conjunctiva as effectively as with the Cytobrush-S, and there were no statistical differences between both groups. AE-3, which is reported as the marker of epithelial cells, were detected quantitatively by a combination of brush cytology and flow cytometry techniques. The result of the present study emphasizes that both the Cytobrush-S and the Accellon-M are valuable for conjunctival brush cytology. An additional positive feature of the Accellon-M may be improved cell collection from the conjunctival epithelium especially when the target cells are in a limited area. The combination of the brush cytology and the flow cytometry technique appears to be a useful adjunct as an additional diagnostic or research tool for use in the detection of various antigens in the conjunctival epithelium.
<title>Differential theory of learning for efficient neural network pattern recognition</title> (1993)

We describe a new theory of differential learning by which a broad family of pattern classifiers (including many well-known neural network paradigms) can learn stochastic concepts efficiently. We describe the relationship between a classifier's ability to generalize well to unseen test examples and the efficiency of the strategy by which it learns. We list a series of proofs that differential learning is efficient in its information and computational resource requirements, whereas traditional probabilistic learning strategies are not. The proofs are illustrated by a simple example that lends itself to closed-form analysis. We conclude with an optical character recognition task for which three different types of differentially generated classifiers generalize significantly better than their probabilistically generated counterparts.
Large-Scale Pyrolysis Oil Production: A Technology Assessment and Economic Analysis (2006)

A broad perspective of pyrolysis technology as it relates to converting biomass substrates to a liquid bio-oil product and a detailed technical and economic assessment of a fast pyrolysis plant.
The new frontier of genome engineering with CRISPR-Cas9 (2014)

The advent of facile genome engineering using the bacterial RNA-guided CRISPR-Cas9 system in animals and plants is transforming biology. We review the history of CRISPR (clustered regularly interspaced palindromic repeat) biology from its initial discovery through the elucidation of the CRISPR-Cas9 enzyme mechanism, which has set the stage for remarkable developments using this technology to modify, regulate, or mark genomic loci in a wide variety of cells and organisms from all three domains of life. These results highlight a new era in which genomic manipulation is no longer a bottleneck to experiments, paving the way toward fundamental discoveries in biology, with applications in all branches of biotechnology, as well as strategies for human therapeutics.
Veterinarians’ role in clients’ decision-making regarding seriously ill companion animal patients (2015)

Different preferences are likely to exist amongst both veterinarians and clients about veterinary involvement in clients' decision-making, and such preferences may vary according to the situation. It is suggested, that one way to handle this challenge is to include respect for client preference on veterinary involvement under a wider understanding of respect for autonomy, and to apply models of shared decision-making to veterinary practice. In any case there is a need to further explore the challenges these situations raise, and for the veterinary profession to engage in more formal and structured deliberation over the role of veterinarians in relation to clients' decision-making.
The Proteomics Protocols Handbook (2005)

Recent developments in the field of proteomics have revolutionized the way that proteins, and their contribution to cellular functions, are studied. The subsequent increased understanding of the mechanisms of cellular function and misfunction will have particular impact in the area of medical research, where disease processes will be better understood, many new (protein) therapeutic targets identified, and novel therapeutic agents developed. At the basic research level, phenotype will be explained in terms of cellular mechanisms.
CD73 and CD39 ectonucleotidases in T cell differentiation: Beyond immunosuppression (2015)

Extracellular ATP is a danger signal released by dying and damaged cells, and it functions as an immunostimulatory signal that promotes inflammation. However, extracellular adenosine acts as an immunoregulatory signal that modulates the function of several cellular components of the adaptive and innate immune response. Consequently, the balance between ATP and adenosine concentration is crucial in immune homeostasis. CD39 and CD73 are two ectonucleotidases that cooperate in the generation of extracellular adenosine through ATP hydrolysis, thus tilting the balance towards immunosuppressive microenvironments. Extracellular adenosine can prevent activation, proliferation, cytokine production and cytotoxicity in T cells through the stimulation of the A2A receptor; however, recent evidence has shown that adenosine may also affect other processes in T-cell biology. In this review, we discuss evidence that supports a role of CD73 and CD39 ectonucleotidases in controlling naive T-cell homeostasis and memory cell survival through adenosine production. Finally, we propose a novel hypothesis of a possible role of these ectonucleotidases and autocrine adenosine signaling in controlling T-cell differentiation.
Vitamin D receptor expression in human lymphocytes. Signal requirements and characterization by western blots and DNA sequencing. (1991)

The signals controlling the expression of the receptor protein for 1 alpha,25-dihydroxyvitamin D3 in normal human lymphocytes and the relationship of this protein to the classical vitamin D receptor were examined. Lymphocytes activated with the OKT3 antibody to the T-cell antigen receptor expressed fewer binding sites as compared to lymphocytes that were activated by the polyclonal activator phytohemagglutinin (PHA). However, combination of OKT3 and phorbol myristate acetate produced a concentration of binding sites similar to the PHA-activated cells. The receptor from OKT3 and OKT3 + phorbol myristate acetate-activated lymphocytes exhibited decreased binding to DNA-cellulose compared to PHA-activated lymphocytes. In lymphocytes activated either by PHA or OKT3 (but not in resting cells), a 50-kDa species cross-reacting with a monoclonal antibody against the intestinal vitamin D receptor was detected. Finally, RNA from activated lymphocytes was amplified by polymerase chain reaction using oligonucleotide primers flanking the 196 base pair long region encoding the DNA-binding domain of the human intestinal receptor. The amplified product showed an identical nucleotide sequence to the DNA-binding domain of the human intestinal receptor. These findings suggest that expression of the 1,25-(OH)2D3 receptor in lymphocytes is triggered by distinct and contingent signals, and that the protein and the mRNA encoding it are identical to the classical vitamin D receptor.
The Lung As an Alternative Route of Delivery for Insulin in Controlling Postprandial Glucose Levels in Patients With Diabetes (1998)

These results suggest that, once plasma glucose levels are normalized, postprandial glucose levels can be maintained below diabetic levels by delivering 1.5 U/kg insulin into the lungs 5 min before the ingestion of a meal.
Renal sympathetic denervation in the aftermath of Symplicity HTN-3 (2014)

status: Published
Dipeptidyl Peptidase-4 Inhibitors (2007)

DPP-4, dipeptidyl peptidase-4; FDA, Food and Drug Administration; GIP, glucosedependent insulinotropic polypeptide; GLP-1, glucagon-like peptide-1
Structural basis of tropism of Escherichia coli to the bladder during urinary tract infection (2002)

The first step in the colonization of the human urinary tract by pathogenic Escherichia coli is the mannose-sensitive binding of FimH, the adhesin present at the tip of type 1 pili, to the bladder epithelium. We elucidated crystallographically the interactions of FimH with D-mannose. The unique site binding pocket occupied by D-mannose was probed using site-directed mutagenesis. All but one of the mutants examined had greatly diminished mannose-binding activity and had also lost the ability to bind human bladder cells. The binding activity of the mono-saccharide D-mannose was delineated from this of mannotriose (Man(alpha 1-3)[Man(alpha 1-6)]Man) by generating mutants that abolished D-mannose binding but retained mannotriose binding activity. Our structure/function analysis demonstrated that the binding of the monosaccharide alpha-D-mannose is the primary bladder cell receptor for uropathogenic E. coli and that this event requires a highly conserved FimH binding pocket. The residues in the FimH mannose-binding pocket were sequenced and found to be invariant in over 200 uropathogenic strains of E. coli. Only enterohaemorrhagic E. coli (EHEC) possess a sequence variation within the mannose-binding pocket of FimH, suggesting a naturally occurring mechanism of attenuation in EHEC bacteria that would prevent them from being targeted to the urinary tract.
The Effect of Code Reordering on Branch Prediction (2000)

Branch prediction accuracy is a very important factor for superscalar processor performance. The ability to predict the outcome of a branch allows the processor to effectively use a large instruction window, and extract a larger amount of Instruction Level Parallelism (ILP). In this paper, we will examine the effect of code layout optimizations on branch prediction accuracy and final processor performance. These code-reordering techniques align branches so that they tend to be not taken, achieving better instruction cache performance and increasing the fetch bandwidth. Here we focus on how these optimizations affect both static and dynamic branch prediction. Code reordering mainly increases the number of not taken branches, which benefits simple static predictors, which reach over 80% prediction accuracy with optimized codes. This branch direction change produces two effects on dynamic branch prediction: on the positive side, trades negative interference for neutral or positive interference in the prediction tables; on the negative side, it causes a worse distribution of the Branch History Register (BHR), causing many possible history values to be unused. Our results show that code reordering reduces negative Pattern History Table (PHT) interference, increasing branch prediction accuracy on small branch predictors. For example, a 0.5KB gshare improves from 91.4% to 93.6%, and a 0.4KB gskew predictor from 93.5% to 94.4%. For larger history lengths, the large amount of not taken branches can degrade predictor performance on dealiased schemes, like the 16KB agree predictor which goes from 96.2% to 95.8%. However, processor performance not only depends on branch prediction accuracy. Layout optimized codes have much better instruction cache performance, and wider fetch bandwidth. Our results show that when all three factors are considered together, code-reordering techniques always improve processor performance. For example, performance still increases by 8% with an agree predictor, which loses prediction accuracy, and it increases by 9% with a gshare predictor, which increases prediction accuracy.
Parallel changes in metabolite and expression profiles in crooked-tail mutant and folate-reduced wild-type mice (2006)

Anomalies in homocysteine (HCY) and folate metabolism are associated with common birth defects and adult diseases, several of which can be suppressed with dietary folate supplementation. Although supplementation reduces the occurrence and severity of neural tube defects (NTDs), many cases are resistant to these beneficial effects. The basis for variable response and biomarkers that predict responsiveness are unknown. Crooked-tail (Cd) mutant mice are an important model of folate-responsive NTDs. To identify features that are diagnostic for responsiveness versus resistance to dietary folate supplementation, we surveyed metabolite and expression levels in liver samples from folate-supplemented, folate-reduced and control diets in Cd mutant and wild-type adult females. Cd homozygotes had normal total homocysteine (tHcy) levels suggesting that folate suppresses NTDs through a mechanism that does not involve modulating serum tHcy levels. Instead, parallel changes in metabolite and expression profiles in folate-supplemented Cd/Cd homozygotes and folate-reduced+/+and Cd/+mice suggest that Crooked-tail homozygotes have a defect in the utilization of intracellular folate. Then, by combining these expression and metabolite profile results with published results for other models and their controls, two clusters were found, one of which included several folate-responsive NTD models and the other previously untested and presumably folate-resistant models. The predictive value of these profiles was verified by demonstrating that NTDs of Ski-/-mutant mice, whose profile suggested resistance to folate supplementation, were not suppressed with dietary folate supplementation. These results raise the possibility of using metabolite and expression profiles to distinguish folate-responsive and resistance adult females who are at risk for bearing fetuses with an NTD.
Epidermal Growth Factor Receptor Tyrosine Kinase Inhibitor–Resistant Disease (2013)

The information presented in this review can guide practitioners and help them inform their patients about EGFR mutations and their impact on the treatment of NSCLC. Efforts should now concentrate on making EGFR-mutant lung cancer a chronic rather than fatal disease.
Prevention of the Hypercontractile Response to Thrombin by Proteinase-Activated Receptor-1 Antagonist in Subarachnoid Hemorrhage (2007)

PAR1 plays a critical role in upregulating PAR1 itself, thereby enhancing the contractile response to thrombin in SAH. PAR1 could thus be a therapeutic target. However, the usefulness of PAR1 antagonist remains to be investigated in vivo.
Radio location in urban CDMA microcells (2002)

A radio location method for code-division multiple-access (CDMA) microcellular networks is investigated. The method discussed focuses on the use of time difference of arrival (TDOA) estimates for deriving the position of a mobile unit in a CDMA system, where the transmitted signal is received by several base stations (BSs). The TDOA estimates are obtained by using a delay-lack loop. A similar method is used in the global position system (GPS), but its performance in an urban microcellular propagation environment has not been previously studied. Simulation results are given for different radio propagation environments.
Polymer‐Induced Heteronucleation for the Discovery of New Extended Solids (2006)

Promoting diversity: Polymer-induced heteronucleation provides kinetic access to three new metal–organic frameworks derived from dicarboxylic acid linkers (see structures). This method is useful as a general approach for discovering extended solids with new topologies that are inaccessible by traditional methods. Supporting information for this article is available on the WWW under http://www.wiley-vch.de/contents/jc_2002/2006/z504312_s.pdf or from the author. Please note: The publisher is not responsible for the content or functionality of any supporting information supplied by the authors. Any queries (other than missing content) should be directed to the corresponding author for the article.
ChemInform Abstract: Synthesis and Study of the Antihypertensive Activity of Substituted N‐Acetylmercaptopropionyl‐6‐(2′‐phenylethyl)pipecolic Acids. (1988)

Abstract Starting with the 6‐methylpicolinic acid ester (I) and the benzaldehydes (II), the N‐acetylmercaptopropionylpipecolic acids (X) and (XI) are prepared as shown in the reaction scheme.
Binding of the synaptic vesicle v-SNARE, synaptotagmin, to the plasma membrane t-SNARE, SNAP-25, can explain docked vesicles at neurotoxin-treated synapses (1997)

Neurotransmitter release requires the specific docking of synaptic vesicles to the presynaptic plasma membrane followed by a calcium-triggered fusion event. Herein we report a previously unsuspected interaction of the synaptic vesicle protein and likely calcium sensor synaptotagmin with the plasma membrane t-SNARE SNAP-25. This interaction appears to resolve the apparent paradox that synaptic vesicles are capable of docking even when VAMP (vesicle-associated membrane protein) or syntaxin is cleaved or deleted and suggests that two species of v-SNAREs (VAMP and synaptotagmin) and two species of t-SNAREs (SNAP-25 and syntaxin) interact to functionally dock synaptic vesicles.
Novel multifunctional PHDCA/PEI nano-drug carriers for simultaneous magnetically targeted cancer therapy and diagnosis via magnetic resonance imaging (2007)

Novel multifunctional magnetic polycation drug carriers (MPDCs) were synthesized to provide simultaneous magnetically targeted cancer therapy and diagnosis via magnetic resonance imaging (MRI). The MPDCs consist of ultra-sensitive magnetic nanocrystals as MR probes and for magnetic targeting, and a chemotherapeutic agent encapsulated in poly(hexadecylcyanoacrylate) (PHDCA) nanoparticles. The PHDCA nanoparticles were further coated with polycationic polyethylenimine (PEI) to enhance cellular uptake efficiency. The MPDCs demonstrated ultra-sensitivity via MRI and sufficient magnetic mobility under an external magnetic field. Drug loading efficiency and release kinetics were also investigated. From the cell viability data, the MPDCs were nontoxic and the doxorubicin hydrochloride (DOX)-loaded MPDCs exhibited excellent tumorcidal efficacy.
Ligand-Independent Toll-like Receptor Signals Generated by Ectopic Overexpression of MyD88 Generate Local and Systemic Antitumor Immunity (2010)

Although critical for initiating and regulating immune responses, the therapeutic use of individual cytokines as anticancer immunotherapeutic agents has achieved only modest clinical success. Consequently, many current strategies have focused on the use of specific immunotherapeutic agonists that engage individual receptors of innate immune networks, such as the Toll-like receptor (TLR) system, each resulting in specific patterns of gene expression, cytokine production, and inflammatory outcome. However, these immunotherapeutics are constrained by variable cellular TLR expression and responsiveness to particular TLR agonists, as well as the specific cellular context of different tumors. We hypothesized that overexpression of MyD88, a pivotal regulator of multiple TLR signaling pathways, could circumvent these constraints and mimic coordinated TLR signaling across all cell types in a ligand-independent fashion. To explore this hypothesis, we generated an adenoviral vector expressing MyD88 and show that Ad-MyD88 infection elicits extensive Th1-specific transcriptional and secreted cytokine signatures in all murine and human cell types tested in vitro and in vivo. Importantly, in vivo intratumoral injection of Ad-MyD88 into established tumor masses enhanced adaptive immune responses and inhibited local tumor immunosuppression, resulting in significantly inhibited local and systemic growth of multiple tumor types. Finally, Ad-MyD88 infection of primary human dendritic cells, tumor-associated fibroblasts, and colorectal carcinoma cells elicited significant Th1-type cytokine responses, resulting in enhanced tumor cell lysis and expansion of human tumor antigen-specific T cells. Thus, Ad-MyD88 initiated robust antitumor activity in established murine tumor microenvironments and in human contexts, suggesting its potential effectiveness as a clinical immunotherapeutic strategy.
Effect of a Long-Acting Somatostatin Analogue (SMS 201–995) on Postprandial Gastric Emptying of <sup>99m</sup>Tc-Tin Colloid and Mouth-to-Caecum Transit Time in Man (1987)

The effect on gut motility of a single subcutaneous injection of 50 μg of the long-acting somatostatin analogue, SMS 201–995, was investigated in 8 normal volunteers who took a drink containing 99mTc and lactulose with a mixed meal. The rate of gastric emptying was assessed by disappearance of the isotope from the stomach area as measured by a gamma camera, and mouth-to-caecum transit time (MCTT) was measured by the appearance of hydrogen in the breath. Gastric emptying was accelerated, with a significant reduction of the time taken to 50% isotope disappearance (37.2 ± 3.3 min during control study vs 23.3 ± 3.4 min after SMS injection; p < 0.01). In contrast, MCTT was prolonged from 57.3 ± 9.4 min (control) to 203.6 ± 14.7 min after SMS (p < 0.001).
Selective Metal Deposition on Photoswitchable Molecular Surfaces (2008)

We report here a novel phenomenon: selective metal deposition on photoswitchable diarylethene (DAE) surfaces. Magnesium vapor was deposited by vacuum evaporation on the colored DAE but not on the uncolored surface. The selective deposition originates in the change of the glass transition temperature of the amorphous DAE film resulting from photoisomerization and therefore from changes of surface molecular motion. We clarified that Mg atoms on the uncolored surface actively migrated on the surface and were desorbed from the surface. The possibility of depositing other metals is also discussed. Light-controllable metal-integrated deposition was demonstrated as a new function of the photoswitchable molecular surfaces. This study reveals new features of the photoswitchable molecular surfaces, and their potential suggests bright prospects for future applications in organic electronics.