gebhart/patrepeval huggingface dataset:
Identification and arrangement of the DNA sequence recognized in specific transformation of Neisseria gonorrhoeae. (1988)

DNA segments from Neisseria gonorrhoeae, cloned and propagated in Escherichia coli, were tested for the ability to competitively inhibit gonococcal transformation. The nucleotide sequences of active segments were determined and compared; these sequences contained the sequence 5' GCCGTCTGAA 3' in common. Subcloning studies confirmed the identity of this sequence as the gonococcal DNA recognition site. The three instances of the recognition sequence isolated from N. gonorrhoeae chromosomal DNA contain the sequence in the immediate neighborhood of its inverted repeat. Because a single copy of the sequence functions as a recognition site, the inverted duplication is not required for specific binding. The dyad symmetric arrangements of the chromosomal recognition sequences may form stable stem-loop structures that can function as terminators or attenuators of transcription. These inverted repeats are located at the boundaries of long open reading frames. The recognition sequence also constitutes part of two other probable terminators of gonococcal genes. We conclude that the signal for recognition of transforming DNA by gonococci is a frequent component of transcriptional terminator sequences. This regulatory function might account for the origin and maintenance of recognition sequences in the chromosomes of Gram-negative transformable bacteria.
Skin Antifreeze Protein Genes of the Winter Flounder, Pleuronectes americanus, Encode Distinct and Active Polypeptides without the Secretory Signal and Prosequences (1996)

Distinct antifreeze polypeptides (AFP) were isolated from the skin of the winter flounder, Pleuronectes americanus, by gel filtration and reverse phase high performance liquid chromatography. In parallel, several cDNA clones were isolated from a skin cDNA library using a liver AFP cDNA probe. Both protein and DNA sequence analyses indicate that flounder skin contains several distinct but homologous alanine-rich AFPs. Although the skin type AFPs contain 11 similar amino acid repeats found in the secretory liver type AFPs, the skin type AFPs are mature polypeptides lacking both the signal and prosequences, indicating that they may function intracellularly. The skin type AFP is significantly less active in thermal hysteretic activity than the liver type AFP. Genomic Southern analysis indicates that like the liver type AFP genes, there are multiple copies (30-40 copies) of skin type AFP. Although the liver type AFP genes are specifically expressed in the liver and to a lesser extent in intestine, the skin type AFP genes are expressed in all tissues examined including the liver and abundantly in exterior tissues, i.e. skin, scales, fin, and gills, suggesting an important protecting role in these exterior tissues.
Class 1 (unique) tumor antigens of human melanoma: partial purification and characterization of the FD antigen and analysis of a mouse polyclonal antiserum. (1987)

Serum antibodies from melanoma patient FD were previously shown to detect a unique antigenic specificity (FD) expressed only on the autologous tumor cells (SK-MEL-131) in culture. The FD determinant is carried by a Mr 90,000 glycoprotein (gp90) that binds to concanavalin A but not to lentil lectin or wheat germ agglutinin. After treatment with endo-N-acetylglucosaminidase H, the antigen no longer bound to concanavalin A. These and other properties indicate the gp90 carries mainly high mannose or hybrid N-linked carbohydrate chains. gp90 was partially purified from a detergent-solubilized membrane preparation by chromatography on DEAE-Sepharose, hydroxylapatite, chelating Sepharose, and lectin-agarose columns. Two-dimensional electrophoresis of the final preparation revealed three major components, one of which was identified as the FD antigen since it was specifically removed by precipitation with serum from patient FD. Immunization with the partially purified antigen preparation elicited anti-gp90 antibodies in two of four mice as demonstrated by sequential radioimmunoprecipitation experiments. Absorption experiments demonstrated that the mouse antibodies could, unlike human FD serum, be absorbed by a number of different cell types. Based on these results it is proposed that gp90 in SK-MEL-131 cells has two distinct epitopes, one, unique, detected by autologous FD serum, and another, common epitope or epitopes, detected by the polyclonal mouse sera. The common epitope(s) is present on gp90 in a variety of cells, including allogeneic melanomas and FD-B cells. These findings, which are compared with those on mouse tumor rejection antigens, have clear implications for the understanding of the nature of tumor antigens.
INHIBITION OF LIPID PEROXIDATION BY N-ACETYLSEROTONIN: IMPLICATIONS IN RETINAL PHYSIOLOGY (1997)

N-Acetylserotonin (NAS) inhibits the peroxidation of linoleic acid induced by a water-soluble initiator, 2,2'-azobis(2-amidinopropane) (ABAP). Lipid peroxidation was detected by the formation of conjugated dienes, monitored spectrophotometrically at 236 nm. N-Acetylserotonin, at concentrations ranging from 200 nM to 20 microM, reduced the rate of ABAP-initiated lipid peroxidation in a concentration-dependent manner. The results of NAS-inhibited lipid peroxidation are compared to the antioxidant activities of melatonin, vitamin E, and a water-soluble vitamin E analog, Trolox. It is suggested that NAS acts as a physiological antioxidant in retinal photoreceptor cells.
Nitric oxide and virus infection (2000)

Nitric oxide (NO) has complex and diverse functions in physiological and pathophysiological phenomena. The mechanisms of many events induced by NO are now well defined, so that a fundamental understanding of NO biology is almost established. Accumulated evidence suggests that NO and oxygen radicals such as superoxide are key molecules in the pathogenesis of various infectious diseases. NO biosynthesis, particularly through expression of an inducible NO synthase (iNOS), occurs in a variety of microbial infections. Although antimicrobial activity of NO is appreciated for bacteria and protozoa, NO has opposing effects in virus infections such as influenza virus pneumonia and certain other neurotropic virus infections. iNOS produces an excessive amount of NO for long periods, which allows generation of a highly reactive nitrogen oxide species, peroxynitrite, via a radical coupling reaction of NO with superoxide. Thus, peroxynitrite causes oxidative tissue injury through potent oxidation and nitration reactions of various biomolecules. NO also appears to affect a host's immune response, with immunopathological consequences. For example, overproduction of NO in virus infections in mice is reported to suppress type 1 helper T-cell-dependent immune responses, leading to type 2 helper T-cell-biased immunological host responses. Thus, NO may be a host response modulator rather than a simple antiviral agent. The unique biological properties of NO are further illustrated by our recent data suggesting that viral mutation and evolution may be accelerated by NO-induced oxidative stress. Here, we discuss these multiple roles of NO in pathogenesis of virus infections as related to both non-specific inflammatory responses and immunological host reactions modulated by NO during infections in vivo.
The continuing evolution of digital cameras and digital photography systems (2002)

Electronic photography became popular when it focused on getting images into PCs, rather than onto TV screens. As desktop computers became image enabled, the sales of digital cameras to both professionals and consumers have grown rapidly. In the past, the primary emphasis was on increasing pixel count. Now that cameras costing less than US $1,000 provide more than 2 million pixels, users are learning that high pixel count is a necessary, but not sufficient condition for photographic quality images. As a result, the focus is shifting to designing optics, sensors, and digital processing to produce cameras having higher ISO speed, lower noise, wider dynamic range, improved tone and color reproduction, and fewer artifacts. Digital image processing can provide product differentiation by both enhancing image quality and providing new features. As pixel count increases, image compression becomes more important. While most digital photography systems today use the current DCT-based JPEG compression, the new wavelet-based JPEG2000 compression standard offers many valuable features for future systems. To support a range of digital photography systems, JPEG2000 will support a range of color interchange spaces and a flexible metadata mechanism.
Desnutrin, an Adipocyte Gene Encoding a Novel Patatin Domain-containing Protein, Is Induced by Fasting and Glucocorticoids (2004)

We have used rat cDNA microarrays to identify adipocyte-specific genes that could play an important role in adipocyte differentiation or function. Here, we report the cloning and identification of a 2.0-kb mRNA coding for a putative protein that we have designated as desnutrin. The novel gene is expressed predominantly in adipose tissue, and its expression is induced early during 3T3-L1 adipocyte differentiation. Desnutrin mRNA levels were regulated by the nutritional status of animals, being transiently induced during fasting. In vitro desnutrin gene expression was up-regulated by dexamethasone in a dose-dependent manner but not by cAMP, suggesting that glucocorticoids could mediate the increase in desnutrin mRNA levels observed during fasting. Desnutrin mRNA codes for a 486-amino acid putative protein containing a patatin-like domain, characteristic of many plant acyl hydrolases belonging to the patatin family. Confocal microscopy of enhanced green fluorescent protein-tagged desnutrin protein-transfected cells showed that the fusion protein localized in the cytoplasm. Moreover, cells overexpressing desnutrin by transfection showed an increase in triglyceride hydrolysis. Interestingly, we also found that the desnutrin gene expression level was lower in ob/ob and db/db obese mouse models. Overall, our data suggest that the newly identified desnutrin gene codes for an adipocyte protein that may function as a lipase and play a role in the adaptive response to a low energy state, such as fasting, by providing fatty acids to other tissues for oxidation. In addition, decreased expression of desnutrin in obesity models suggests its possible contribution to the pathophysiology of obesity.
Purification of a unique glycoprotein that enhances phenol oxidase activity in scorpion (Heterometrus bengalensis) haemolymph (1989)

A monomeric glycoprotein (SGP) of Mr 32,000 was isolated to purity from scorpion (Heterometrus bengalensis) haemolymph by (NH4)2SO4 fractionation, chromatofocusing and h.p.l.c. The homogeneity of SGP is confirmed by polyacrylamide-gel electrophoresis. SGP is soluble in 100%-satd. (NH4)2SO4 solution. Needle-shaped crystals of SGP were obtained in an aqueous environment. The glycan part of the molecule contains arabinose, which does not commonly occur in animal glycoproteins. Amino acid analysis demonstrated a preponderance of glycine, tyrosine and glutamic acid. SGP enhances phenol oxidase (EC 1.14.18.1) activity.
Color gamut mapping and the printing of digital color images (1988)

Principles and techniques useful for calibrated color reproduction are defined. These results are derived from a project to take digital images designed on a variety of different color monitors and accurately reproduce them in a journal using digital offset printing. Most of the images printed were reproduced without access to the image as viewed in its original form; the color specification was derived entirely from calorimetric specification. The techniques described here are not specific to offset printing and can be applied equally well to other digital color devices. The reproduction system described is calibrated using CIE tristimulus values. An image is represented as a set of three-dimensional points, and the color output device as a three-dimensional solid surrounding the set of all reproducible colors for that device, called its gamut . The shapes of the monitor and the printer gamuts are very different, so it is necessary to transform the image points to fit into the destination gamut, a process we call gamut mapping . This paper describes the principles that control gamut mapping. Included also are some details on monitor and printer calibration, and a brief description of how digital halftone screens for offset printing are prepared.
Phytotoxicity and Distribution of Sorgoleone in Grain Sorghum Germplasm (1996)

The relative phytotoxicity of sorgoleone as measured by seed germination and seedling growth of selected crop and weed species and inhibition of photosynthetic oxygen evolution in atrazine-resistant and -susceptible cell cultures of potato (Solanum tuberosum L.) and common groundsel (Senecio vulgaris L.) were investigated. Relatively little or no effect of sorgoleone was observed on radicle elongation at concentrations less than 500 μM in Petri dish bioassays. Sorgoleone was very phytotoxic to large crabgrass (Digitatia sanguinalis), with a GR50 of 10 μM for shoot growth in a hydroponic culture bioassay. Inhibition of shoot and root growth of velvetleaf (Abutilon theophrasti) and barnyardgrass (Echinocloa crus-galli) was also observed at higher concentrations ranging from 10 to 200 μM, but ivyleaf morningglory (Ipomea hederacea) was tolerant. Sorgoleone inhibited photosynthetic oxygen evolution in both susceptible and resistant cell cultures of potato and common groundsel, and the effect was similar to that of diuron, a strong inhibitor of PS II electron transport. Chlorophyll fluorescence response to sorgoleone in both resistant and susceptible cell cultures was nearly the same. Grain sorghum (Sorghum bicolor L. Moench) genotypes varied considerably in the amount of sorgoleone produced. Root exudates generally contained 85−90% pure sorgoleone on the basis of HPLC analysis. These data indicate that sorgoleone is phytotoxic at micromolar concentrations, exhibits marked selectivity, and inhibits photosynthetic electron transport similar to diuron. Keywords: Sorgoleone; bioassay; hydroponics; inhibition; phytotoxicity; photosynthetic oxygen evolution; electron transport; root exudate
Demodex-associated Folliculitis (1998)

To the Editor: I appreciated R. Vollmer's interesting study, published in the American Journal of Dermatopathology in 1996 (1). I published a comparable study in 1986 (2) and am glad to find that Dr. Vollmer found similar results. I analyzed 69 skin biopsies, each containing at least 3 Demodex. He analyzed 24 biopsies, containing at least 1 Demodex. I found Demodex in 56% of inflamed follicles (n = 287) and in only 29% of noninflamed follicles (n = 423) (p < 0.001). He found Demodex in 42% of inflamed follicles (n = 208) and in only 10% of non-inflamed follicles (n = 180) (p < 0.0009). I found inflammation in 57% of follicles with Demodex (n = 284) and in 29% of follicles without Demodex (n = 426) (p < 0.001). He found inflammation in 83% of follicles with Demodex (n = 105) and in 43% of follicles without Demodex (n = 283) (p < 0.0009). Dr. Vollmer writes: "The most elegant study to relate the number of mites to clinical rosacea was that of Bonnar et al. (3)." I published a comparable study in the same year, 1993, also with cyanoacrylate glue, and introduced the concept of standardized skin surface biopsy to evaluate the Demodex density (4). I was also glad to find that Bonnar et al.'s results were comparable with mine. I appreciate the interesting study of Dr. Vollmer, but I do not understand why he did not refer to my first nor my second work, which are both closely related to his study and his discussion. Fabienne Forton, M.D. Brussels, Belgium
In Vivo Expression of an Interferon-α Gene by Intramuscular Injection of Naked DNA (1997)

Acid-stable type I interferons belong to a multigene family. The biologic relevance of each subtype in vivo remains unknown. We have developed an experimental model in which muscles were transfected in situ with naked DNA plasmids encoding an IFN transgene to assess the roles of individual IFN subtypes in vivo. Murine IFN-alpha 9 gene was subcloned into several mammalian expression vectors. Adult C57BL/6 mice were injected bilaterally in regenerating tibialis anterior muscles with naked DNA 5 days after muscle injury to enhance DNA uptake and expression. In the muscles of mice given the IFN-alpha 9 plasmid constructs, acid-stable IFNs were detected by bioassay using reduction in cytopathic effect of encephalomyocarditis virus-infected L929 cells. In these same muscles, IFN-alpha 9 transcripts were identified by RT-PCR, indicating that transcription had occurred. Acid-stable IFNs were detected from days 7 to 28 post-DNA inoculation. Furthermore, these proteins were found in the sera of DNA-inoculated mice. Control groups of mice given the blank expression vectors did not produce detectable IFNs in muscle or sera as determined by bioassay, nor were transcripts detected by RT-PCR. This approach now allows investigation of the effector function of individual subtypes in various murine disease models.
Effects of Native Type II Collagen Treatment on Knee Osteoarthritis: A Randomized Controlled Trial (2015)

All in all, these results suggest that native type II collagen treatment combined with acetaminophen is superior to only acetaminophen for symptomatic treatment of patients with knee osteoarthritis.
'Other' breast cancer susceptibility genes: searching for more holy grail (2001)

While germline mutations in BRCA1 and BRCA2 account for most, if not all families with autosomal dominant transmission of susceptibility to both breast and ovarian cancer, it has become clear that together these genes only account for a small proportion of hereditary site-specific breast cancer susceptibility. However, difficulties due to genetic heterogeneity, reduced penetrance and perhaps gene mutation frequency complicate ongoing efforts to identify additional susceptibility genes. Therefore, multiple approaches are being used to identify additional high and low penetrance genes. Families with three or more breast cancer cases are being used in traditional linkage studies, which are expected to yield only moderate or high penetrance susceptibility genes. Breast cancer case-control studies are being used to look for genetic variants or polymorphisms that confer an increased risk of breast cancer in a wide variety of cellular pathways, ranging from the detoxification of environmental carcinogens to steroid hormone metabolism, DNA damage repair and immune surveillance, an approach useful primarily to identify low penetrance susceptibililty genes. However, neither approach has yielded convincing results to date. A third approach, using BRCA1 and BRCA2 mutation carriers to identify genes that are associated with modification of breast cancer risk has met with some limited success, perhaps because effects on breast cancer risk in BRCA1 and BRCA2 mutation carriers are more readily detected in smaller studies, given the much higher number of events in these cohorts at very high risk of breast cancer. Clearly, hereditary breast cancer susceptibility is a complex phenomenon, in which multiple genes may play a role. It will be necessary to use all of these approaches, as well as more comprehensive genomic studies, to identify additional breast cancer-related genes.
Comparative field study evaluating the activity of recombinant factor VIII Fc fusion protein in plasma samples at clinical haemostasis laboratories (2013)

Discrepancies exist for some of the modified coagulation factors when assayed with different one-stage clotting and chromogenic substrate assay reagents. The aim of this study was to evaluate the performance of a recombinant factor VIII Fc fusion protein (rFVIIIFc), currently in clinical development for the treatment of severe haemophilia A, in a variety of one-stage clotting and chromogenic substrate assays in clinical haemostasis laboratories. Haemophilic plasma samples spiked with rFVIIIFc or Advate(®) at 0.05, 0.20 or 0.80 IU mL(-1) were tested by 30 laboratories using their routine procedures and plasma standards. Data were evaluated for intra- and inter-laboratory variation, accuracy and possible rFVIIIFc-specific assay discrepancies. For the one-stage assay, mean recovery was 95% to 100% of expected for both Advate(®) and rFVIIIFc at 0.8 IU mL(-1). Intra-laboratory percent coefficient of variance (CV) ranged from 6.3% to 7.8% for Advate(®), and 6.0% to 10.3% for rFVIIIFc. Inter-laboratory CV ranged from 10% for Advate(®) and 16% for rFVIIIFc at 0.8 IU mL(-1), to over 30% at 0.05 IU mL(-1) for both products. For the chromogenic substrate assay, the average FVIII recovery was 107% ± 5% and 124% ± 8% of label potency across the three concentrations of Advate(®) and rFVIIIFc, respectively. Plasma rFVIIIFc levels can be monitored by either the one-stage or the chromogenic substrate assay routinely performed in clinical laboratories without the need for a product-specific rFVIIIFc laboratory standard. Accuracy by the one-stage assay was comparable to that of Advate(®), while marginally higher results may be observed for rFVIIIFc when using the chromogenic assay.
Technique for measuring the refractive index and its change with temperature in the infrared* (1975)

A simple method for measuring refractive index in the infrared is described. It uses autocollimation from the front surface of a prism and requires only that the receiver be moved to measure a new deviated ray when either the wavelength of the source or the temperature of the sample is changed. An error analysis that includes consideration of the evacuated sample space and wedge in the chamber windows shows that errors as low as one part in the fourth decimal place can be obtained.
Symbolic model checking: an approach to the state explosion problem (1992)

Finite state models of concurrent systems grow exponentially as the number of components of the system increases. This is known widely as the state explosion problem in automatic verification, and has limited finite state verification methods to small systems. To avoid this problem, a method called symbolic model checking is proposed and studied. This method avoids building a state graph by using Boolean formulas to represent sets and relations. A variety of properties characterized by least and greatest fixed points can be verified purely by manipulations of these formulas using Ordered Binary Decision Diagrams. Theoretically, a structural class of sequential circuits is demonstrated whose transition relations can be represented by polynomial space OBDDs, though the number of states is exponential. This result is born out by experimental results on example circuits and systems. The most complex of these is the cache consistency protocol of a commercial distributed multiprocessor. The symbolic model checking technique revealed subtle errors in this protocol, resulting from complex execution sequences that would occur with very low probability in random simulation runs. formal verification, temporal logic, model checking, state explosion problem, symbolic model checking, binary decision diagrams. cache consistency, cache coherence. protocol verification. hardware description languages, SMV, asynchronous circuits, Petri nets. occurrence nets, process invariants.
TREATMENT OF RENAL ALLOGRAFT REJECTION WITH T10B9.1A31 OR OKT3 (1997)

T10B9 provides treatment for renal allograft acute cellular rejection as effective as that of OKT3 with fewer untoward effects, less cytokine release and nephropathy, fewer serious infections, and without increased development of human anti-mouse antibody. The lack of cross-reactivity offers an alternative therapy should the first mAb fail or re-rejection occur. A phase III trial should be initiated in renal allograft recipients, and phase I and phase II trials should be initiated in other solid-organ transplantations.