gebhart/patrepeval huggingface dataset:
High‐speed photodamage cell selection using a frequency‐doubled argon ion laser (1995)

A flow cytometer was developed for the high-speed "sorting" of desired cells by selectively irradiating (zapping) the undesired cells from a population. After previous efforts to photoinactivate cells with photosensitizers had failed, it was decided to exploit the photosensitivity of the cell's DNA at 257 nm. It was shown that a 257 nm laser output power of 20-100 mW was sufficient to induce a 4.5 log cell kill after the cells were processed through a focused 257 nm laser beam. Experiments proved that the photodamage flow cytometer (ZAPPER) could selectively photoinactivate cells at rates over 22,000 events/s, and selection purities ranged from 81% to 100%. The yields of the desired cells depended on the selection mode. In the Enrichment mode, the zap laser was not aimed at the jet, and only undesired cells were exposed to a brief ultraviolet (UV) pulse after modulation of the UV laser beam. The yields of desired cells ranged from 95% to 105%. In the Purge mode, the zap laser beam was aimed onto the jet, and only desired cells were allowed to pass after deflection of the UV laser beam; the yields of desired cells ranged from 12% to 52%. The cause of the reduced yields in the PURGE mode was traced to the fact that the Electro-Optic Modulator was used to modulate the zap laser proved too slow for the intended application. The lifetime of the frequency-doubling crystal used for the generation of the 257 nm beam was found to be limited to several days.(ABSTRACT TRUNCATED AT 250 WORDS)
Discovery of 8-Hydroxyadenines as a Novel Type of Interferon Inducer (2002)

9-Benzyl-8-hydroxyadenine (6) was found to possess interferon-inducing activity in vitro as a lead compound. Although replacement of the 9-benzyl group of 6 did not improve the activity, the introduction of a substituent such as alkyl, alkylthio, alkylamino, and alkoxy groups into the 2-position of the adenine ring resulted in a remarkable increase in the activity. The 2-alkylthio (30-32), 2-butylamino (41), and 2-butoxy (47) analogues indicated the highest activities by oral administration to mice.
Immunosuppressive and Anti-inflammatory Properties of Interleukin 10 (1995)

Interleukin 10 (IL-10) indirectly prevents antigen-specific T-cell activation, which is associated with downregulation of the antigen presentation and accessory cell functions of monocytes, macrophages, Langerhans cells and dendritic cells. In addition, IL-10 inhibits T-cell expansion by directly inhibiting IL-2 production by these cells. These properties of IL-10, together with its capacity to downregulate the production of proinflammatory cytokines and chemokines by activated monocytes, polymorphonuclear leucocytes and eosinophils, indicate that IL-10 is a potent immunosuppressant in vitro. IL-10 has similar activities in vivo. It inhibits lipopolysaccharide or staphylococcal enterotoxin B induced lethal shock in mice. In addition, IL-10 deficient mice develop chronic inflammatory bowel disease, which could be reduced, or prevented by IL-10 treatment. IL-10 also prevented the development of colitis in a SCID mouse model. Collectively, these data indicate that IL-10 has great potential therapeutical utility in the treatment of diseases, such as chronic inflammation, autoimmune diseases, transplant rejection, graft-versus-host disease and sepsis.
Redox Control of Renal Function and Hypertension (2008)

Loss of redox homeostasis and formation of excessive free radicals play an important role in the pathogenesis of kidney disease and hypertension. Free radicals such as reactive oxygen species (ROS) are necessary in physiologic processes. However, loss of redox homeostasis contributes to proinflammatory and profibrotic pathways in the kidney, which in turn lead to reduced vascular compliance and proteinuria. The kidney is susceptible to the influence of various extracellular and intracellular cues, including the renin-angiotensin-aldosterone system (RAAS), hyperglycemia, lipid peroxidation, inflammatory cytokines, and growth factors. Redox control of kidney function is a dynamic process with reversible pro- and anti-free radical processes. The imbalance of redox homeostasis within the kidney is integral in hypertension and the progression of kidney disease. An emerging paradigm exists for renal redox contribution to hypertension.
Transcriptional Profiling ofhigh pigment-2dgTomato Mutant Links Early Fruit Plastid Biogenesis with Its Overproduction of Phytonutrients (2007)

Phenotypes of the tomato (Solanum lycopersicum) high pigment-2(dg) (hp-2(dg)) and hp-2(j) mutants are caused by lesions in the gene encoding DEETIOLATED1, a negative regulator of light signaling. Homozygous hp-2(dg) and hp-2(j) plants display a plethora of distinctive developmental and metabolic phenotypes in comparison to their normal isogenic counterparts. These mutants are, however, best known for the increased levels of carotenoids, primarily lycopene, and other plastid-accumulating functional metabolites. In this study we analyzed the transcriptional alterations in mature-green, breaker, and early red fruits of hp-2(dg)/hp-2(dg) plants in relation to their normal counterparts using microarray technology. Results show that a large portion of the genes that are affected by hp-2(dg) mutation display a tendency for up- rather than down-regulation. Ontology assignment of these differentially regulated transcripts revealed a consistent up-regulation of transcripts related to chloroplast biogenesis and photosynthesis in hp-2(dg) mutants throughout fruit ripening. A tendency of up-regulation was also observed in structural genes involved in phytonutrient biosynthesis. However, this up-regulation was not as consistent, positioning plastid biogenesis as an important determinant of phytonutrient overproduction in hp-2(dg) and possibly other hp mutant fruits. Microscopic observations revealed a highly significant increase in chloroplast size and number in pericarp cells of mature-green hp-2(dg)/hp-2(dg) and hp-2(j)/hp-2(j) fruits in comparison to their normal counterparts. This increase could be observed from early stages of fruit development. Therefore, the molecular trigger that drives phytonutrient overproduction in hp-2(dg) and hp-2(j) mutant fruits should be initially traced at these early stages.
Influence of membrane potential on calcium efflux from giant axons of Loligo. (1986)

Experiments are described in which Ca efflux is monitored in axons under voltage clamp. As Ca efflux consists of more than one component, conditions were sought where one component predominates. Thus external Na-dependent Ca efflux can be studied in relative isolation either at pH 9.0 or in fully poisoned axons immersed in Ca-free media; external Ca-dependent Ca efflux can be studied in fully poisoned axons immersed in Na-free media and the Na-independent, energy requiring, pump is best examined in Na and Ca-free sea waters. Both in unpoisoned axons at pH 9.0 and fully poisoned axons at pH 7.8, the external Na-dependent Ca efflux is activated by hyperpolarization and inhibited by depolarization. Depolarizations achieved either electrically or by exposure to high K are roughly comparable and the inhibition brought about by high K can largely be removed by electrical hyperpolarization to the initial resting potential. In both Na sea waters and choline sea waters containing 100 mM-Na, Ca efflux is increased e-fold over approximately 50 mV. In choline sea water, external Ca-dependent Ca efflux from fully poisoned axons is unaffected by voltage over the range -80 to -30 mV. But addition of K or Li activates the flux and this activation is increased by hyperpolarization and decreased by depolarization, suggesting that the activating cation may also be transported into the axon. The Na-independent, energy-requiring, flux is inhibited by electrical hyperpolarization and stimulated by electrical depolarization. External K also stimulates the flux and part of this stimulation can be removed by electrical hyperpolarization. These data show that the energy-dependent pump is sensitive to membrane potential in the physiological range and suggest that it may be an electrogenic process. The finding that voltage affects the energy-dependent (uncoupled) pump and external Na-dependent fluxes in opposite directions may help explain why the total Ca efflux from intact axons responds to potential in a very variable manner.
Metabolic modelling and engineering of Escherichia coli for succinate production (2010)

Thesis submitted in fulfillment of the requirements for the degree of doctor (PhD) in applied biological sciences
Management Ergolect as a Separate Language Variety (1997)

Management is one of those social groups which are in position to create and maintain their social image through verbal means. Verbal communication in management is to a great extent employed to attain this goal and the function of management ergolect (ME) is expected to be predominantly social. Research, based on a computational analysis of two text corpora totaling 150 000 running words, has shown that ME possesses a recognizable identity of its own with two prominent tendencies, both of which confirm the thesis of the prevailingly social function of ME: on the lexical level this is manifested through the choice and use of key words and concepts and on the stylistic level in the metaphor generating network of ME. By building its own semiotic system and using it to communicate the principles of the social group and its culturological and civilisational values, ME goes beyond the limits of a business transaction and exists as a separate linguistic, rhetorical and social entity.
Translational Mini-Review Series on B cell subsets in disease. Transitional B cells in systemic lupus erythematosus and Sjögren's syndrome: clinical implications and effects of B cell-targeted therapies (2011)

Systemic lupus erythematosus (SLE) and Sjögren's syndrome are autoimmune disorders which are characterized by a disturbed B cell homeostasis which leads ultimately to dysfunction of various organs. One of the B cell subsets that appear in abnormal numbers is the population of transitional B cells, which is increased in the blood of patients with SLE and Sjögren's syndrome. Transitional B cells are newly formed B cells. In mice, transitional B cells undergo selection checks for unwanted specificity in the bone marrow and the spleen in order to eliminate autoreactive B cells from the circulating naive B cell population. In humans, the exact anatomical compartments and mechanisms of the specificity check-points for transitional B cells remain unclear, but appear to be defective in SLE and Sjögren's syndrome. This review aims to highlight the current understanding of transitional B cells and their defects in the two disorders before and after B cell-targeted therapies.
The mechanism of cobalt biosorption (1989)

Nonliving biomass of the common seaweed Ascophyllum nodosum is capable of accumulating cobalt from aqueous solutions to the extent of 160 mg Co(2+)/g. Successful desorption of cobalt from the biomass by acidic CaCl(2) solutions revealed that the metal uptake phenomenon is reversible, implying physical sorption of cobalt. Chemical and instrumental analysis including electron microscopy, infrared (IR) spectroscopy, X-ray dispersion and diffraction analysis provided supporting evidence that the biosorption mechanism involves predominantly ion exchange. Alginates of the cell wall (-COOH groups) play an important role in cobalt binding. Coordination and sorption in the cell wall structure occur simultaneously and rapidly whereas penetration of cobalt into the cell occurs at a lower rate.
Opportunities and obstacles for deep learning in biology and medicine (2017)

Abstract Deep learning, which describes a class of machine learning algorithms, has recently showed impressive results across a variety of domains. Biology and medicine are data rich, but the data are complex and often ill-understood. Problems of this nature may be particularly well-suited to deep learning techniques. We examine applications of deep learning to a variety of biomedical problems—patient classification, fundamental biological processes, and treatment of patients—and discuss whether deep learning will transform these tasks or if the biomedical sphere poses unique challenges. We find that deep learning has yet to revolutionize or definitively resolve any of these problems, but promising advances have been made on the prior state of the art. Even when improvement over a previous baseline has been modest, we have seen signs that deep learning methods may speed or aid human investigation. More work is needed to address concerns related to interpretability and how to best model each problem. Furthermore, the limited amount of labeled data for training presents problems in some domains, as do legal and privacy constraints on work with sensitive health records. Nonetheless, we foresee deep learning powering changes at both bench and bedside with the potential to transform several areas of biology and medicine.
Protecting Browsers from Extension Vulnerabilities (2010)

Browser extensions are remarkably popular, with one in three Firefox users running at least one extension. Although well-intentioned, extension developers are often not security experts and write buggy code that can be exploited by malicious web site operators. In the Firefox extension system, these exploits are dangerous because extensions run with the user's full privileges and can read and write arbitrary files and launch new processes. In this paper, we analyze 25 popular Firefox extensions and find that 88% of these extensions need less than the full set of available privileges. Additionally, we find that 76% of these extensions use unnecessarily powerful APIs, making it difficult to reduce their privileges. We propose a new browser extension system that improves security by using least privilege, privilege separation, and strong isolation. Our system limits the misdeeds an attacker can perform through an extension vulnerability. Our design has been adopted as the Google Chrome extension system.
Risk Factors for Open-angle Glaucoma (1995)

In the Barbados Eye Study black population, persons most likely to have open-angle glaucoma were older men and had a family history of open-angle glaucoma, high intraocular pressure, lean body mass, and cataract history. These results suggest the importance of possible genetic or familial factors in open-angle glaucoma. The role of vascular risk factors is consistent with our finding of low blood pressure to intraocular pressure relationships, but the results could be explained by the high intraocular pressure in open-angle glaucoma.
Variable-wavelength switchable Bragg gratings formed in polymer-dispersed liquid crystals (2001)

We report a holographic polymer-dispersed liquid crystal cell whose reflection peak can be tuned as a function of applied voltage. Electro-optic results are presented which are in excellent agreement with our model based on coupled wave theory.
Palladium-catalyzed Displacement of Aryl Halide by Tin Analogue of Reformatsky Reagent (1985)

Abstract Reaction of ethyl α-(tributylstannyl)acetate with aryl bromides in the presence of zinc bromide or chloride and a catalytic amount of dichlorobis(tri-o-tolylphosphine)palladium was found to give ethyl arylacetates in good yields except with the aryl bromide having p-acetyl or p-nitro group.
One fungus, which genes? Development and assessment of universal primers for potential secondary fungal DNA barcodes (2015)

The aim of this study was to assess potential candidate gene regions and corresponding universal primer pairs as secondary DNA barcodes for the fungal kingdom, additional to ITS rDNA as primary barcode. Amplification efficiencies of 14 (partially) universal primer pairs targeting eight genetic markers were tested across > 1 500 species (1 931 strains or specimens) and the outcomes of almost twenty thousand (19 577) polymerase chain reactions were evaluated. We tested several well-known primer pairs that amplify: i) sections of the nuclear ribosomal RNA gene large subunit (D1-D2 domains of 26/28S); ii) the complete internal transcribed spacer region (ITS1/2); iii) partial β -tubulin II (TUB2); iv) γ-actin (ACT); v) translation elongation factor 1-α (TEF1α); and vi) the second largest subunit of RNA-polymerase II (partial RPB2, section 5-6). Their PCR efficiencies were compared with novel candidate primers corresponding to: i) the fungal-specific translation elongation factor 3 (TEF3); ii) a small ribosomal protein necessary for t-RNA docking; iii) the 60S L10 (L1) RP; iv) DNA topoisomerase I (TOPI); v) phosphoglycerate kinase (PGK); vi) hypothetical protein LNS2; and vii) alternative sections of TEF1α. Results showed that several gene sections are accessible to universal primers (or primers universal for phyla) yielding a single PCR-product. Barcode gap and multi-dimensional scaling analyses revealed that some of the tested candidate markers have universal properties providing adequate infra- and inter-specific variation that make them attractive barcodes for species identification. Among these gene sections, a novel high fidelity primer pair for TEF1α, already widely used as a phylogenetic marker in mycology, has potential as a supplementary DNA barcode with superior resolution to ITS. Both TOPI and PGK show promise for the Ascomycota, while TOPI and LNS2 are attractive for the Pucciniomycotina, for which universal primers for ribosomal subunits often fail.
Whole Genome Amplification and De novo Assembly of Single Bacterial Cells (2009)

The methods describe in this paper will be useful for sequencing genomes of individual cells from a variety of samples.
Interaction of polyglutamyl derivatives of methotrexate, 10-deazaaminopterin, and dihydrofolate with dihydrofolate reductase. (1986)

Polyglutamyl derivatives of methotrexate (MTX) and 10-deazaaminopterin (10-DAM) containing a total of one through six glutamate residues (Glu residues) were tested as inhibitors of dihydrofolate reductase (DHFR) derived from sheep, chicken, and beef liver. The ability of dihydropteroylpentaglutamate to antagonize the inhibitory activity of these analogues was also studied. The most striking effects were seen with sheep liver DHFR, where polyglutamylation of MTX causes stepwise decreases in the concentration required for 50% inhibition (IC50) with each additional Glu residue until MTX with a total of six Glu residues has an IC50 value 1/3 that of MTX. With 10-DAM the pattern is more complex. The IC50 values increase with addition of Glu residues until a maximum is reached with 10-DAM having a total of three Glu residues which has a value twice that of 10-DAM. 10-DAM with a total of four Glu residues and 10-DAM with a total of five Glu residues have progressively lower IC50 values, the latter being equipotent with 10-DAM. With dihydropteroylpentaglutamate as substrate instead of dihydrofolate, the IC50 values are increased 2- to 5-fold for both MTX and 10-DAM derivatives. The results obtained with chicken liver and beef liver DHFR are generally similar to those described for the sheep liver enzyme, but the effects of polyglutamylation are less pronounced. The addition of 0.2 M KCl to the assay system reduces the differences in inhibitory potency of the polyglutamyl derivatives with all three enzymes tested. We conclude that polyglutamylation can alter the interaction of folate analogues and dihydrofolate with DHFR.
Novel combined miniature optical coherence tomography ultrasound probe for in vivo intravascular imaging (2011)

We have developed a miniature integrated optical coherence tomography (OCT) ultrasound (US) probing system for intravascular imaging applications. In the OCT probe, the light coming out of a single mode fiber is focused by a gradient-index lens and then reflected by a right-angle prism from the side of the probe into the sample. It was combined with a 35 MHz PMN-PT side-viewing ultrasound transducer to obtain the ultrasound image as well. The OCT and ultrasound probes were integrated as a single probe to obtain OCT and ultrasound images simultaneously. The integrated probe has an outer diameter of 0.69 mm which, to our knowledge, is the smallest integrated OCT-US probe reported. Fast data acquisition and processing was implemented for real-time imaging. In vitro OCT and US images of human coronary artery with pathology, as well as in vivo images of normal rabbit abdominal aorta, were obtained using the integrated OCT-US probe to demonstrate its capability.
Long-term Remission of Malignant Brain Tumors after Intracranial Infection: A Report of Four Cases (1999)

The case histories presented in conjunction with the relevant literature reviewed support the concept that microbial infections may influence immune responses in brain tumor defense.
The value of CD64 expression in distinguishing acute myeloid leukemia with monocytic differentiation from other subtypes of acute myeloid leukemia: a flow cytometric analysis of 64 cases. (2007)

Strong CD64 expression distinguishes AML M5; however, heterogeneous, dim, or moderate expression in itself does not distinguish M0 through M4 subtypes from M5 with dim to moderate CD64 expression. However, any CD64 expression associated with strong CD15 expression distinguishes AML M4 or M5, from other AML subtypes.
Miniature Mass Spectrometers (2009)

We discuss miniaturization in mass spectrometry in terms of the mass analyzer, the mass spectrometer, and the total analytical system. Mass analyzer miniaturization has focused on ion traps. Decreases in mass analyzer size facilitate reduction of the sizes of the other components of a miniature mass spectrometer, especially the radio frequency electronics and vacuum system. Appropriate sample introduction systems are needed for performance optimization. The criteria by which a miniature mass spectrometer is judged include adequate performance in the traditional areas of resolution, detection limits, and specificity; ruggedness; reliability; and fully autonomous operation. Our discussion of the total analytical system emphasizes the removal of the bottleneck of sample preparation and suggests a solution to the combination of sampling, preconcentration, and ionization: ambient ionization methods. We also describe current miniature mass spectrometers.
INGN-225: a dendritic cell-based p53 vaccine (Ad.p53-DC) in small cell lung cancer: observed association between immune response and enhanced chemotherapy effect (2010)

INGN-225 is safe, induces a significant immune response, and appears to sensitize SCLC to subsequent chemotherapy. Improvements in immune response induction and understanding the chemotherapy-immunotherapy synergism will determine INGN-225's future role as an anticancer therapy.
Syntheses and Immunologic Properties of Escherichia coli O157 O-Specific Polysaccharide and Shiga Toxin 1 B Subunit Conjugates in Mice (1999)

Escherichia coli O157 is the major cause of diarrhea-associated hemolytic uremic syndrome (HUS). Strains causing HUS contain either Shiga toxin 1 (Stx1) or Stx2, or both. In adult volunteers, conjugate vaccines of detoxified lipopolysaccharide (LPS) elicited bactericidal antibodies to E. coli O157. Here, the detoxified LPS was conjugated with improved schemes to the nontoxic B subunit of Stx1. Mice injected with these bivalent conjugates elicited both bactericidal antibodies to E. coli O157 and neutralization antibodies to Stx1.
Tapered section of multimode cladded fibers as mode filters and mode analyzers (1975)

Mode filtering characteristics of biconical tapers in multimode fibers were examined. The insertion loss of a biconical taper for the HE11 mode is 0.2 dB and the rejection ratios for higher−order modes are more than 20 dB. The mode conversion in a biconical taper is sufficiently small except for the HE1n modes. It is found that a linearly tapered section can be used as a mode analyzer for multimode fibers.