gebhart/patrepeval huggingface dataset:
A gold-nanoparticle-based fluorescence resonance energy transfer probe for multiplexed hybridization detection: accurate identification of bio-agents DNA (2007)

We report a gold-nanoparticle-based miniaturized, inexpensive and battery-operated ultra-sensitive fluorescence resonance energy transfer (FRET) probe for screening biological agents DNA at the femtomolar level. We demonstrate a hybridization detection method using multicolor oligonucleotide-functionalized organic dyes and gold nanoparticles as nanoprobes. In the presence of various target sequences, detection of sequence-specific DNA is possible via an independent hybridization process. As proof of concept, multiplexed detection of two target sequences, (1)?oligonucleotide sequence associated with the anthrax lethal factor and (2) sequence related to positions 1027?1057 of the E.?coli 23S rDNA, have been demonstrated with high sensitivity and specificity. The quenching efficiency as a function of distance is investigated. The mechanism of distant dependence fluorescence quenching has been discussed.
Rumen contents as a reservoir of enterohemorrhagic Escherichia coli (1993)

We investigatedthe role of the rumen fermentation as a barries to the foodborne pathogen, Escherichia coli O157:H7. Strains of E. coli, including several isolates of O157:H7, grew poorly in media which simulated the ruminal environment of a well-fed animal. Strains of E. coli O157:H7 did not display a superior tolerance to ruminal conditions which may facilitate their colonization of the bovine digestive tract. Unrestricted growth of E. coli was observed in rumen fluid collected from fasted cattle. Growth was inhibited by rumen fluid collected from well-fed animals. Well-fed animals appear less likely to become reservoirs for pathogenic E. coli. These results have implications for cattle slaughter practices and epidemiological studies of E. coli O157:H7.
A New Method for Axial Decay Function Calibration of Evanescent Field in Multi-Angle Total Internal Reflection Fluorescence Microscopy (2016)

Three-dimensional image reconstruction in multi-angle total internal reflection fluorescence microscopy relies on actual penetration depths of evanescent wave at various incidence angles. In this paper, we propose a simple and elegant calibration method to calculate the actual axial decay profile of a given evanescent field, for the analytical solution of theoretical equation is hard to solve in complicated conditions. The results calculated by the proposed method agree with the experimental demands in our research. Our calibration method, together with multi-angle TIRF imaging, permits 3D reconstruction of cell surface in superb axial resolution.
Expression of a flower-specific Myb protein in leaf cells using a viral vector causes ectopic activation of a target promoter. (1995)

The promoter of the bean PAL2 gene (encoding phenylalanine ammonia-lyase; EC 4.3.1.5) is a model for studies of tissue-restricted gene expression in plants. Petal epidermis is one of the tissues in which this promoter is activated in tobacco. Previous work suggested that a major factor establishing the pattern of PAL2 expression in tobacco petals is the tissue distribution of a protein closely related to Myb305, which is a Myb-like transcriptional activator from snapdragon. In the present work, we show that Myb305 expression in tobacco leaves causes ectopic activation of the PAL2 promoter. To achieve Myb305 expression in planta, a viral expression vector was used. This approach combines the utility of transient assays with the possibility of direct biochemical detection of the introduced factor and may have wider application for studying the function of plant transcription factors.
Exhumation of high‐pressure metamorphic rocks during crustal extension in the D'Entrecasteaux region, Papua New Guinea (1993)

Abstract The D'Entrecasteaux Islands of eastern Papua New Guinea consist of a number of active metamorphic core complexes formed under an extensional tectonic setting related to sea‐floor spreading in the west Woodlark Basin. The complexes are defined by mountainous domes (>2500 m high) of fault‐bounded, high‐grade metamorphic rocks (including eclogite facies) intruded by 2–4‐Ma granodiorite plutons. Garnet–clinopyroxene exchange thermometers indicate that the temperature of equilibration of the eclogites was 730–900° C. The jadeite component of omphacite indicates minimum pressure of 21 kbar, suggesting depths of >70 km. The metamorphic rocks have undergone widespread retrogression to amphibolite facies. Retrogression of the metamorphic basement is associated with shearing and formation of the metamorphic core complexes. P–T conditions in the early stages of shear zone activity, determined using the garnet–biotite exchange thermometer and the GASP and GRIPS barometers, were 570–730° C and 7–11 kbar. A second phase of re‐equilibration at much lower pressures appears to be related to the widespread intrusion of granodiorite plutons. One re‐equilibrated gneiss indicated maximum temperature of 730° C at estimated pressures of approximately 4 kbar. This late, high‐temperature metamorphism is also indicated by reactions involving the production of hercynite and corundum in aluminous gneisses and formation of sillimanite at the expense of kyanite. Two major episodes of granodiorite intrusion occurred during uplift and exhumation of the core complexes. Both closely coincide spatially with high‐temperature metamorphic rocks, the onset of deformation in extensional shear zones and subsequent uplift of the metamorphic basement. These observations indicate a fundamental link between uplift and granodiorite intrusion during continental extension and the formation of the D'Entrecasteaux Islands metamorphic core complexes.
Metoclopramide therapy in fifty-five patients with delayed gastric emptying. (1980)

Fifty-five patients with delayed gastric emptying and the symptoms of nausea, vomiting, postprandial bloating and early satiety were treated with metoclopramide. Obstruction was excluded by upper endoscopy and standard upper gastrointestinal series. None were on medication known to retard gastric emptying. All patients had an abnormal barium burger radiologic study. Twenty-one patients had had previous vagotomy and drainage procedure, five had diabetic gastroparesis and 29 had idiopathic delayed gastric emptying. Metoclopramide significantly decreased the symptom scores of the surgical and idiopathic patients. When all patients were analyzed together, there was a significant improvement in both the metoclopramide and placebo treated patients. When, however, the improvement on metoclopramide was compared to the improvement on placebo, there was a significant metoclopramide effect beyond the placebo effect. Thus, metoclopramide is an effective agent in treating the symptom-complex of patients with delayed gastric emptying.
Preliminary Fertility Results with Frozen Bovine Spermatozoa (1955)

The fertility of bovine spermatozoa frozen in a concentrated form (200 × 106 motile spermatozoa per milliliter of extender), thawed at 5° C. at the bull stud, further extended to approximately 10 × 106 motile spermatozoa per milliliter and used for breeding 24 to 60 hours later, was compared with that of semen frozen in single-breeding vials. The latter were thawed at the farm just prior to insemination. The split sample technique was used with two ejaculates from three different bulls. Prefreezing processing and freezing procedures were slightly modified from those reported by Polge et al. and Dunn et al. Unfrozen semen processed in the conventional manner was used for the control breedings. All semen was extended to provide 8 to 10 million motile spermatozoa per insemination, though estimates made later indicated that actual numbers varied between 4 and 14 million. The 60- to 90-day nonreturns to first services were as follows: unfrozen control, 459 services, 74.5%; frozen "concentrated," 449 services, 51.7%; frozen as single breeding samples and stored one day at −79° C., 55 services, 72.7%; frozen as single breeding samples and stored 103 days at −79° C., 92 services, 77.0%.
A uniform framework for processing temporal object queries (2002)

The paper explores a uniform framework for processing temporal queries in the context of object oriented databases. A temporal object data model is developed by extending the unified model of RDBs and OODBs from UniSQL/X with a time dimension, that forms temporal relational-like cubes but with aggregation and inheritance hierarchies. A query algebra is thereby defined to provide an access of objects through these associations of aggregation, inheritance and time reference. Due to the hierarchy of the data model and reducibility of the query algebra, an extensible approach to processing temporal object queries within the uniform query processing framework is attained. A set of transformation rules is identified for query rewrite, that includes the known relational and object rules plus those pertaining to the time reference. To evaluate temporal queries involved in the path, a decomposition strategy is proposed. It has been shown that temporal object queries can be processed and optimized within the uniform query processing framework.
L-carnitine inhibits ethanol-induced gastric mucosal injury in rats. (2010)

L-carnitine is a quaternary amine that is essential for the normal oxidation of long-chain fatty acids by mitochondria. It is known that L-carnitine and its derivatives prevent the formation of reactive oxygen species, scavenge free radicals and protect cells from peroxidative stress. Oxygen-derived free radicals and lipid peroxidation products play a critical role in the pathogenesis of ethanol-induced gastric mucosal injury. The aim of the present study was to determine the effect of L-carnitine on lipid peroxidation induced by ethanol in the rat stomach. In our study, gastric mucosal injury was induced by the intragastric administration of 1 ml of absolute ethanol. Test compounds were given to rats by gavage 30 min before the ethanol administration. The animals were killed 60 min after the administration of ethanol. The stomach of each animal was removed. Mucosal damage was evaluated by macroscopic examination, histological analysis and by measurement of lipid peroxidation and glutathione activity. The intragastric administration of ethanol induced hyperemia and hemorrhagic erosions in the rat stomachs. L-carnitine significantly prevented gastric ulcerogenesis induced by ethanol and decreased the ulcer index. Plasma and gastric lipid peroxidation that was increased significantly by ethanol was decreased after treatment with L-carnitine. Ethanol treatment decreased significantly the gastric glutathione levels, and pretreatment with L-carnitine increased them significantly. Based on these data, the beneficial effects of L-carnitine on ethanol-induced gastric mucosal injury may be attributed to its antiperoxidative effects.
Pensioned off? (1982)

From time to time in Physics Bulletin, you report the results of successive salary surveys made from a cross section of members of The Institute of Physics. For me and many, if not most, in my age group these are purely of academic interest, serving only to create envy in those who, like me, are living on pensions with no inflation-proofing.
Low-noise four-terminal ac resistance bridge (1985)

The results of a detailed noise calculation for a resistance bridge are presented. These results allow one to adapt the design of the bridge to any particular need, while maintaining optimized performance. A bridge has been built based on these results. The measured relative sensitivity of this bridge (2×10−5 with only 10 pW dissipated in the sensor) is ∼40% better than the best previous published results. With minor changes it is shown that this sensitivity can be improved by a factor of 3.
Therapeutic Down-Modulators of Staphylococcal Superantigen-Induced Inflammation and Toxic Shock (2010)

Staphylococcal enterotoxin B (SEB) and related superantigenic toxins are potent stimulators of the immune system and cause a variety of diseases in humans, ranging from food poisoning to toxic shock. These toxins bind directly to major histocompatibility complex (MHC) class II molecules on antigen-presenting cells and specific Vβ regions of T-cell receptors (TCR), resulting in hyperactivation of both monocytes/macrophages and T lymphocytes. Activated host cells produce massive amounts of proinflammatory cytokines and chemokines, activating inflammation and coagulation, causing clinical symptoms that include fever, hypotension, and shock. This review summarizes the in vitro and in vivo effects of staphylococcal superantigens, the role of pivotal mediators induced by these toxins in the pathogenic mechanisms of tissue injury, and the therapeutic agents to mitigate the toxic effects of superantigens.
Protein Transduction of Dendritic Cells for NY-ESO-1-Based Immunotherapy of Myeloma (2005)

Myeloma vaccines, based on dendritic cells pulsed with idiotype or tumor lysate, have been met with limited success, probably in part due to insufficient cross-priming of myeloma antigens. A powerful method to introduce myeloma-associated antigens into the cytosol of dendritic cells is protein transduction, a process by which proteins fused with a protein transduction domain (PTD) freely traverse membrane barriers. NY-ESO-1, an immunogenic antigen by itself highly expressed in 60% of high-risk myeloma patients, was purified to near homogeneity both alone and as a recombinant fusion protein with a PTD, derived from HIV-Tat. Efficient entry of PTD-NY-ESO-1 into dendritic cells, confirmed by microscopy, Western blotting, and intracellular flow cytometry, was achieved without affecting dendritic cell phenotype. Experiments with amiloride, which inhibits endocytosis, and N-acetyl-l-leucinyl-l-norleucinal, a proteasome inhibitor, confirmed that PTD-NY-ESO-1 entered dendritic cells by protein transduction and was degraded by the proteasome. Tetramer analysis indicated superior generation of HLA-A2.1, CD8+ T lymphocytes specific for NY-ESO-1(157-165) with PTD-NY-ESO-1 compared with NY-ESO-1 control protein (44% versus 2%, respectively). NY-ESO-1-specific T lymphocytes generated with PTD-NY-ESO-1 secreted IFN-gamma indicative of a Tc1-type cytokine response. Thus, PTD-NY-ESO-1 accesses the cytoplasm by protein transduction, is processed by the proteasome, and NY-ESO-1 peptides presented by HLA class I elicit NY-ESO-1-specific T lymphocytes.
Thermal Modifications in Softwood Studied by FT‐IR and UV Resonance Raman Spectroscopies (2004)

Abstract Scots pine planks were heat‐treated under steam in a temperature range of 100–240°C at every 20°C. Changes in chemical structure of the wood samples were examined with UV resonance Raman (UVRR) and Fourier transform infrared (FT‐IR) spectroscopies. Prior to the FT‐IR and UVRR analysis, the heartwood part of wood samples were ground and extracted with acetone. Both the extracts and the extracted samples were analyzed. In addition, Klason lignin contents of the samples were determined. The FT‐IR and UVRR spectroscopy were powerful techniques to monitor chemical changes in the heat‐treated wood samples. Results confirmed most of what determined previously by other research groups using different techniques. The UVRR and FT‐IR spectra of acetone extracts showed that lignin became partly acetone soluble after a heat treatment of 180°C or greater. Increased levels of free phenolic hydroxyl groups were detected in lignin, probably due to cleavages of β‐O‐aryl ether interunit linkages. The amount of extractable lignin increased with increasing temperature, while the resin in the extracts decreased. UVRR spectra of the wood samples extracted with acetone indicated that the structure of unextractable lignin remained unchanged when heated up to 200°C. Formation of new carbonyl structures was observed in solid wood samples and their extracts. These structures were possibly formed from the degradation products of lignin and hemicelluloses. Lignin content of the samples was increased as a result of degradation of wood hemicelluloses, which started below 200°C.
Synthesis and FTIR characterization of some dextran sulphates (2005)

The result of the synthesis and investigation of FTIR spectra of some dextran sulphates and their sodium (Na) salts are presented. A synthesis was conducted (under different reaction parameters) of esters with various degrees of esterification (from 1.0 to 2.3). FTIR investigations were performed on sulphates of low and high molecular hydrogenated dextrans of various molecular masses (Mw of 5000, 7000, 8000, 40000 and 500000). Particular care was taken to determine the degree of linearity of the synthesized dextran sulphates, the conformation of glucopyranosyl units and the way the sulpho groups and the water were bonded in their structures.
Combination dabrafenib and trametinib in the management of advanced melanoma with BRAFV600 mutations (2016)

Combination therapy with dabrafenib and trametinib improves response rate, progression-free survival and overall survival when compared to dabrafenib or vemurafenib alone. The addition of trametinib to dabrafenib changes the adverse event profile, making hyperkeratosis and cutaneous squamous cell carcinomas less common but side effects such as fever and nausea more common. How dabrafenib/trametinib is best sequenced with other effective treatments such as immune checkpoint blockade remains uncertain.
Developmental expression of the mouse <i>Evx-2</i> gene: relationship with the evolution of the HOM/Hox complex (1994)

The mouse Evx-2 gene is located in the immediate vicinity of the Hoxd-13 gene, the most posteriorly expressed gene of the HOXD complex. While the Evx-1 gene is also physically linked to the HOXA complex, it is more distantly located from the corresponding Hoxa-13 gene. We have analysed the expression of Evx-2 during development and compared it to that of Evx-1 and Hoxd-13. We show that, even though Evx-2 is expressed in the developing CNS in a pattern resembling that of other Evx-related genes, the overall expression profile is similar to that of the neighbouring limbs and genitalia. We propose that the acquisition of expression features typical of Hox genes, together with the disappearance of some expression traits common to Evx genes, is due to the close physical linkage of Evx-2 to the HOXD complex, which results in Evx-2 expression being partly controlled by mechanisms acting in the HOX complex. This transposition of the Evx-2 gene next to the Hoxd-13 gene may have occurred soon after the large scale duplications of the HOX complexes. A scheme is proposed to account for the functional evolution of eve-related genes in the context of their linkage to the HOM/Hox complexes.
A MUTATIONAL ANALYSIS OF THE TRIPLO-LETHAL REGION OF <i>DROSOPHILA MELANOGASTER</i> (1979)

The extensive analysis of the impact of segmental aneuploidy by Lindsley et al. (1972) showed that there are relatively few haplo-lethal loci in the genome and that, with one exception, all loci are triplo-viable. The exceptional locus, which lies in salivary gland chromosome region 83D-E, is associated with lethality when present in either one or three doses in an otherwise diploid individual (Denell 1976). The genetic nature of the phenomenon has been studied by examining the rates of induction, by ionizing radiation and chemical mutagens, of mutations affecting the dose-sensitive behavior. For both types of mutagens, the frequency of inactivation of the locus is relatively low, and a high proportion of such mutations is associated with chromosomal deficiencies. These data indicate that the locus is infrequently and perhaps never inactivated by a DNA base-pair substitution and thus that the triplo-lethal phenomenon is not associated with a "typical" structural gene. It is possible that the triplo-lethal locus is very small, is reiterated or otherwise complex or is functionally insensitive to base-pair substitutions. The result that all mutations that complement a duplication of the triplo-lethal locus are lethal in heterozygous combination with a normal third chromosome argues that triplo- and haplo-lethality are concomitants of the same phenomenon. Salivary gland chromosome analysis of newly induced deficiencies and duplications localizes the locus to 83D4,5--83E1,2, and further cytogenetic mapipulation shows that the dose-sensitive behavior is independent of the position of the locus in the genome.
Chaotic Image Scrambling Algorithm Based on S-DES (2006)

With the security requirement improvement of the image on the network, some typical image encryption methods can't meet the demands of encryption, such as Arnold cat map and Hilbert transformation. S-DES system can encrypt the input binary flow of image, but the fixed system structure and few keys will still bring some risks. However, the sensitivity of initial value that Logistic chaotic map can be well applied to the system of S-DES, which makes S-DES have larger random and key quantities. A dual image encryption algorithm based on S-DES and Logistic map is proposed. Through Matlab simulation experiments, the key quantities will attain 1017 and the encryption speed of one image doesn't exceed one second. Compared to traditional methods, it has some merits such as easy to understand, rapid encryption speed, large keys and sensitivity to initial value.
Interindividual and Interethnic Variation in Genomewide Gene Expression: Insights into the Biological Variation of Gene Expression and Clinical Implications (2009)

Genomewide analysis of gene expression variation demonstrated biological differences among transcripts. Transcripts with the least biological variation are better candidates for reference genes, whereas those with low interindividual variation may be good disease markers. The presence of interethnic variation suggests that ethnicity-specific reference intervals may be necessary.
Importance of ALDH1A enzymes in determining human testicular retinoic acid concentrations (2014)

Retinoic acid (RA), the active metabolite of vitamin A, is required for spermatogenesis and many other biological processes. RA formation requires irreversible oxidation of retinal to RA by aldehyde dehydrogenase enzymes of the 1A family (ALDH1A). While ALDH1A1, ALDH1A2, and ALDH1A3 all form RA, the expression pattern and relative contribution of these enzymes to RA formation in the testis is unknown. In this study, novel methods to measure ALDH1A protein levels and intrinsic RA formation were used to accurately predict RA formation velocities in individual human testis samples and an association between RA formation and intratesticular RA concentrations was observed. The distinct localization of ALDH1A in the testis suggests a specific role for each enzyme in controlling RA formation. ALDH1A1 was found in Sertoli cells, while only ALDH1A2 was found in spermatogonia, spermatids, and spermatocytes. In the absence of cellular retinol binding protein (CRBP)1, ALDH1A1 was predicted to be the main contributor to intratesticular RA formation, but when CRBP1 was present, ALDH1A2 was predicted to be equally important in RA formation as ALDH1A1. This study provides a comprehensive novel methodology to evaluate RA homeostasis in human tissues and provides insight to how the individual ALDH1A enzymes mediate RA concentrations in specific cell types.