gebhart/patrepeval huggingface dataset:
Retinoic acid and steroids inhibit Epstein-Barr virus-induced nuclear antigen, DNA synthesis and lymphocyte transformation. (1985)

Retinoic acid, dexamethasone and prednisolone were evaluated for their effects on Epstein-Barr virus (EBV)-induced nuclear antigen (EBNA), DNA synthesis and transformation of human thymus-independent, B lymphocytes. It was found that continuous treatment of target cells with these agents completely inhibited EBV-induced transformation events. However, discontinuous treatment of the virus-infected cultures with these agents resulted in the recovery of DNA synthesis, and the appearance of EBNA and transformation. When the cells were treated with these agents 8 days after the virus infection, the inhibitors had no effect. These results show that only continuous treatment with these agents inhibited EBV-mediated transformation; these inhibitors had no effect once the EBNA and EBV-induced DNA synthesis were initiated in target lymphocytes.
Mutational inactivation of an inhibitory sequence in human immunodeficiency virus type 1 results in Rev-independent gag expression (1992)

We have characterized an inhibitory RNA element in the human immunodeficiency virus type 1 (HIV-1) gag coding sequence that prevents gag expression. The inhibition exerted by this element could be overcome by the presence of the Rev-responsive element in cis and of Rev protein in trans. To understand the mechanism of function, we inactivated the inhibitory element by mutagenesis while maintaining an intact gag coding region. A constitutive high level of Rev-independent gag expression was achieved only after the introduction of 28 point mutations over a large region of 270 nucleotides within the gag coding region. To our knowledge, this is the first demonstration of inactivation of a negative RNA element within a coding region without alteration of the expressed protein. Elimination of the inhibitory element in the p17gag region, named INS-1, offered the opportunity to detect a second inhibitory element in the gag-pol region. The presence of either INS element is sufficient to inhibit gag expression, demonstrating that multiple INS elements acting independently can inhibit HIV RNA expression. Expression of gag from Rous sarcoma virus, a retrovirus that does not require Rev-like regulatory proteins, revealed that the Rous sarcoma virus p19gag region does not contain inhibitory elements. These results demonstrate the presence of a strong inhibitory element acting at the level of mRNA and provide a general method for the removal of such elements from mRNA coding regions. The inhibitory element functions in the absence of any HIV-1 proteins, suggesting that cellular factors are responsible for this inhibition.
Ground Penetrating Radar Measurements in a Controlled Vadose Zone: Influence of the Water Content (2004)

Ground penetrating radar (GPR) is a nondestructive method, which, as with other geophysical methods, has been successfully used to estimate the water content or hydraulic properties of soils. We performed GPR measurements to calibrate and compare water content estimates with actual water contents in a sand box. A vadose zone was simulated by injecting water in a sand box. We obtained four GPR data sets: for dry sand, for sand with water tables at 72‐ and 48‐cm depths, and for sand after drainage. Using the reflections (or diffractions) from the bottom of the sand box (or objects buried in the sand), mean relative dielectric permittivities were determined at several depths in the sand box. These relative dielectric permittivities were used to calculate “real” mean relative dielectric permittivities of a sand box made up of three layers (dry sand, unsaturated sand, and fully saturated sand), knowing that a layer can be subdivided into more layers depending on the depth of the reflections (or diffractions) recorded. We used three relationships between relative dielectric permittivity and the water content to estimate the mean water content for each layer. From these water contents and the known volume of sand considered, we estimated the amount of water in the sand box for each water table. Subtracting the volume obtained for dry sand from the volume obtained for the different water tables gave estimates of the variations in water quantities in the sand box; these were compared with the quantities injected in the sand box. Despite uncertainties in the determination of the mean relative dielectric permittivities, the calculated variations in water quantities were very similar to those injected in the sand box.
Experimental study on skin surface character utilizing laser Doppler effect (2002)

In this paper, the study on roughness of skin surface utilizing laser Doppler effect is put forward. Theoretically speaking, the roughness can be regard as the synthesis of longitudinal and transverse displacement of a point on epidermis. In the paper, the fundamentals and method of displacement measurement utilizing laser Doppler effect are introduced, and the theoretical system of skin surface cognition utilizing laser Doppler effect is established. The system design of skin surface character testing is extracted, a new reference optical system is put forward to achieve the roughness detection, an optical grating is used for frequency mixing and getting high SNR signals in this measurement. The factors influencing the measurement accuracy are expounded. Moreover, the theory analysis and experiment-based methods are offered to improve the accuracy. The measurement technique utilizing laser Doppler effect has many advantages, such as high precision, quickly response speed, large measurement range and non-touch measurement, so this study can be applied in analyzing the profile and distortion of skin surface, which is very important in theory and practice for the non-invasive detection fields ofbiology and iatrology.
Localization of an antiviral site on the pregnancy recognition hormone, ovine trophoblast protein 1. (1990)

Ovine trophoblast protein 1 (oTP-1) is the interferon alpha (IFN-alpha) variant with potent antiviral activity and low toxicity that is responsible for maternal recognition of pregnancy in sheep. To examine the structure/function basis for the potent antiviral activity of oTP-1, we have exploited the direct approach of synthetic peptide competition with oTP-1 for receptor, using N-terminal oTP-1-(1-37) and C-terminal oTP-1-(139-172) peptides. These peptides possess structures similar to those predicted for the intact molecule on the basis of circular dichroism. oTP-1-(1-37) at 1.5 mM specifically blocked oTP-1 antiviral activity without affecting the antiviral activity of natural ovine IFN-alpha, recombinant bovine IFN-alpha, and recombinant human IFN-alpha. At concentrations as low as 0.15 mM, oTP-1-(139-172) blocked the antiviral activity of oTP-1, as well as that of natural ovine IFN-alpha, recombinant bovine IFN-alpha, and recombinant human IFN-alpha, but not recombinant bovine interferon gamma. Further, binding of radiolabeled oTP-1 to endometrial membrane preparations could be effectively inhibited by polyclonal anti-C-terminal and anti-N-terminal antisera, with the anti-C-terminal antiserum being the more effective inhibitor. Consistent with peptide and antiserum functional data, oTP-1 and recombinant bovine IFN-alpha are predicted to possess similar C-terminal structure but different N-terminal structure by composite surface profile predictions. The findings suggest that the C-terminal regions of IFN-alpha s bind to a common site on the IFN-alpha receptor while the N-terminal region binds to a site unique for the particular IFN-alpha.
Internet telescopes: capabilities and benchmarks (2010)

In this golden age of small-telescope astronomy, the term 'armchair astronomer' has an entirely new significance. High-quality, low-cost optics have combined with advances in imaging-array technologies and sophisticated, electronic servomotor mounts to place in-struments of exceptional power and effectiveness in the hands of amateurs. Some of these instruments are exceptionally powerful and well-sited; many represent hundreds of thou-sands of dollars in investment and even larger commitments in owner/operator time. Open standards such as those in the ASCOM initiative (Web: ASCOM) have enabled automation components from many different manufacturers to work together in a more-or-less integrated fashion. The results are fully-automated, serious-amateur telescopes quite capable of variable star work, supernovae searches, and even detecting extrasolar planets. In the past few years, the control software and interfaces to these automated telescopes have become exceptionally sophisticated, surpassing professional control software at least in beauty and design, if not in raw functionality. Most of these interfaces can function through the Internet. Armchair astronomy, indeed!
Magnesium Cardioplegia Enhances mRNA Levels and the Maximal Velocity of Cytochrome Oxidase I in the Senescent Myocardium During Global Ischemia (1995)

K and/or Mg cardioplegia ameliorates [Ca2+]mt accumulation in aged hearts during normothermic global ischemia and increases COX I mRNA levels to a level not significantly different from that found in mature hearts.
A novel mouse model of Niemann–Pick type C disease carrying a D1005G-Npc1 mutation comparable to commonly observed human mutations (2011)

We have identified a point mutation in Npc1 that creates a novel mouse model (Npc1(nmf164)) of Niemann-Pick type C1 (NPC) disease: a single nucleotide change (A to G at cDNA bp 3163) that results in an aspartate to glycine change at position 1005 (D1005G). This change is in the cysteine-rich luminal loop of the NPC1 protein and is highly similar to commonly occurring human mutations. Genetic and molecular biological analyses, including sequencing the Npc1(spm) allele and identifying a truncating mutation, confirm that the mutation in Npc1(nmf164) mice is distinct from those in other existing mouse models of NPC disease (Npc1(nih), Npc1(spm)). Analyses of lifespan, body and spleen weight, gait and other motor activities, as well as acoustic startle responses all reveal a more slowly developing phenotype in Npc1(nmf164) mutant mice than in mice with the null mutations (Npc1(nih), Npc1(spm)). Although Npc1 mRNA levels appear relatively normal, Npc1(nmf164) brain and liver display dramatic reductions in Npc1 protein, as well as abnormal cholesterol metabolism and altered glycolipid expression. Furthermore, histological analyses of liver, spleen, hippocampus, cortex and cerebellum reveal abnormal cholesterol accumulation, glial activation and Purkinje cell loss at a slower rate than in the Npc1(nih) mouse model. Magnetic resonance imaging studies also reveal significantly less demyelination/dysmyelination than in the null alleles. Thus, although prior mouse models may correspond to the severe infantile onset forms of NPC disease, Npc1(nmf164) mice offer many advantages as a model for the late-onset, more slowly progressing forms of NPC disease that comprise the large majority of human cases.
Hypoxemia during Sleep in Duchenne Muscular Dystrophy (1988)

Overnight polysomnography after acclimatization was performed on 14 patients with Duchenne muscular dystrophy (mean age, 18.3 yr; mean VC, 1.24 L). Despite their lack of sleep-related symptoms and normal daytime blood gas tensions, periods of hypopnea and/or apnea (H/A) were observed in all patients (mean frequency 9.6/h; range, 3.7 to 17.0; mean duration 23.1; range of means, 16 to 36 s). In 9 patients, between 0.5 and 12.3 oxygen desaturations of greater than 5% occurred per hour, with falls from a mean SaO2 baseline of 95.4 +/- 0.6% (SEM) to a mean nadir of 74.2 +/- 3.9% (range, 58 to 90). This desaturating group (n = 9) showed longer and more frequent H/A than did the 5 nondesaturators; the proportion of REM sleep occupied by H/A was 37.7 +/- 3.8% in the desaturating group compared with only 15.1 +/- 5.1% in the remainder (p less than 0.01). The severity of sleep-disordered breathing could not be reliably predicted from daytime pulmonary function test results, and only maximal static expiratory pressure appeared significantly lower in the desaturating group. Hypopneas were associated with reduced chest wall movement in all subjects, and with chest wall paradox in one; continued submental "inspiratory" EMG activity throughout "central" apneas in 2 subjects suggested that these episodes were not truly central in origin. Sleep hypoxemia is imputed in the progression of several chronic respiratory diseases, and its prevention in Duchenne and related neuromuscular diseases may influence morbidity and mortality.
Design, fabrication and testing of microlens arrays for sensors and microsystems (1997)

We report on our activities in design, fabrication, characterization and system integration of refractive microlens arrays for sensors and microsystems. Examples for chemical analysis systems (, blood gas sensor), neural networks and multiple pupil imaging systems for photolithography (microlens and smart mask lithography) are presented.
Myosin heavy chain gene expression in human heart failure. (1997)

Two isoforms of myosin heavy chain (MyHC), alpha and beta, exist in the mammalian ventricular myocardium, and their relative expression is correlated with the contractile velocity of cardiac muscle. Several pathologic stimuli can cause a shift in the MyHC composition of the rodent ventricle from alpha- to beta-MyHC. Given the potential physiological consequences of cardiac MyHC isoform shifts, we determined MyHC gene expression in human heart failure where cardiac contractility is impaired significantly. In this study, we quantitated the relative amounts of alpha- and beta-MyHC mRNA in the left ventricular free walls (LVs) of 14 heart donor candidates with no history of cardiovascular disease or structural cardiovascular abnormalities. This group consisted of seven patients with nonfailing (NF) hearts and seven patients with hearts that exhibited donor heart dysfunction (DHD). These were compared with 19 patients undergoing cardiac transplantation for chronic end-stage heart failure (F). The relative amounts of alpha-MyHC mRNA to total (i.e., alpha + beta) MyHC mRNA in the NF- and DHD-LVs were surprisingly high compared with previous reports (33.3+/-18.9 and 35.4+/-16.5%, respectively), and were significantly higher than those in the F-LVs, regardless of the cause of heart failure (2.2+/-3.5%, P < 0.0001). There was no significant difference in the ratios in NF- and DHD-LVs. Our results demonstrate that a considerable amount of alpha-MyHC mRNA is expressed in the normal heart, and is decreased significantly in chronic end-stage heart failure. If protein and enzymatic activity correlate with mRNA expression, this molecular alteration may be sufficient to explain systolic dysfunction in F-LVs, and therapeutics oriented towards increasing alpha-MyHC gene expression may be feasible.
Sensitive microplate enzyme-linked immunosorbent assay for detection of antibodies against the scrub typhus rickettsia, Rickettsia tsutsugamushi (1979)

A microtiter enzyme-linked immunosorbent assay (ELISA) has been developed for the titration of antibodies against scrub typhus in human and animal sera. Scrub typhus rickettsiae were grown in monolayers of irradiated mouse LM3 cells and separated from host cell materials by differential centrifugation, filtration through a glass filter (AP-20, Millipore Corp.), and isopycnic banding in Renografin density gradients. The scrub typhus ELISA antigens were obtained from the purified viable rickettsiae by French pressure cell disruption and addition of 0.2% Formalin to the soluble extract. Antisera prepared in rabbits against the prototype Karp, the Kato, and the Gilliam strains of scrub typhus were used to standardize the ELISA and to compare its sensitivity and specificity to that of the indirect fluorescent antibody test (IFA). ELISA titers were measured as the greatest serum dilution showing an optical density 0.25 above controls or by the optical density achieved at a fixed serum dilution. The IFA and ELISA end point titers were quite similar, and all three measures of titer had comparable specificity for the strains of scrub typhus. No cross-reactions between the typhus and scrub typhus wera were observed by ELISA. Both the immunoglobulin M (IgM) and IgG antibody titers of 12 sequential sera from four patients with scrub typhus were obtained by IFA and ELISA. The IFA and ELISA end point titers for IgM and IgG had correlation coefficients of 0.91 and 0.97, respectively, whereas the ELISA optical density values at a serum dilution of 1:100 had slightly lower correlations with IFA titers (0.80 and 0.94). Early rising IgM titers followed by rising IgG titers were demonstrated by ELISA in three patients with primary scrub typhus infections, whereas the IgG response predominated in a patient with a reinfection. It is concluded that the ELISA for scrub typhus is a very satisfactory alternative to the IFA test.
Dysregulation of Nrf2 Signaling in Diabetes: An Opportunity for a Multitarget Approach (2015)

Oxidative stress is a central feature of diabetes and plays a causal role in the pathogenesis of diabetic complications. The nuclear factor-like 2 (Nrf2) transcription factor mediates the induction of antioxidant and cytoprotective genes and is a major regulator of the endogenous antioxidant and detoxification systems. Multiple aspects of the Nrf2 signaling pathway are aberrant in diabetes and simultaneously targeting the dysregulated aspects of the Nrf2 signaling pathway ought to be considered.
Nitrosative stress elicited by nNOSµ delocalization inhibits muscle force in dystrophin‐null mice (2010)

The mechanism of force reduction is not completely understood in Duchenne muscular dystrophy (DMD), a dystrophin-deficient lethal disease. Nitric oxide regulates muscle force. Interestingly, neuronal nitric oxide synthase µ (nNOSµ), a major source of muscle nitric oxide, is lost from the sarcolemma in DMD muscle. We hypothesize that nNOSµ delocalization contributes to force reduction in DMD. To test this hypothesis, we generated dystrophin/nNOSµ double knockout mice. Genetic elimination of nNOSµ significantly enhanced force in dystrophin-null mice. Pharmacological inhibition of nNOS yielded similar results. To further test our hypothesis, we studied δ-sarcoglycan-null mice, a model of limb-girdle muscular dystrophy. These mice had minimal sarcolemmal nNOSµ delocalization and muscle force was less compromised. Annihilation of nNOSµ did not improve their force either. To determine whether nNOSµ delocalization itself inhibited force, we corrected muscle disease in dystrophin-null mice with micro-dystrophins that either restored or did not restore sarcolemmal nNOSµ. Similar muscle force was obtained irrespective of nNOSµ localization. Additional studies suggest that nNOSµ delocalization selectively inhibits muscle force in dystrophin-null mice via nitrosative stress. In summary, we have demonstrated for the first time that nitrosative stress elicited by nNOSµ delocalization is an important mechanism underlying force loss in DMD.
Increased Cortical Bone Content of Insulin-Like Growth Factors in Acromegalic Patients1 (1999)

To investigate cortical bone composition and the role of the insulin-like growth factor (IGF) system in active acromegaly, iliac crest bone biopsies were obtained from 15 patients (3 women and 12 men), aged 21-64 yr (mean, 45.6 yr), and 25 age- and sex-matched controls (8 women and 17 men), aged 22-66 yr (mean, 44.6 yr). Levels of IGF-I, IGF-II, IGF-binding protein-3 (IGFBP-3), IGFBP-5, and total protein were determined in extracts obtained after ethylenediamine tetraacetate and guanidine hydrochloride extraction. Osteocalcin and calcium were determined in extracts after HCl hydrolysis. Cortical bone contents of IGF-I, IGF-II, and IGFBP-5 were significantly elevated in the acromegalic patients compared with control values [91% (P < 0.001), 44% (P < 0.04), and 115% (P < 0.004), respectively]. There was no significant difference in IGFBP-3, osteocalcin, protein, and calcium between patients and controls. This study suggests that the increased levels of growth factors in cortical bone from acromegalics is a reflection of local production, secondary to a chronic systemic excess of GH and IGF-I.
Scanning Mutagenesis Using T4 DNA Ligase and Short Degenerate DNA Oligonucleotides Containing Tri-nucleotide Mismatches (2002)

Scanning mutagenesis is an attractive tool for protein structure-function correlation analysis. With one round of this method it is possible to obtain a library containing all possible single-residue mutants of the protein of interest. The practical application of this approach is currently limited by the large number and cost of the required 30-35mer oligonucleotides. As an alternative, we studied the ligation of shorter DNA oligonucleotides (6-11mer) containing a degenerate binding site and a desired mutation mismatch to a nested set of megaprimers annealed to the gene of interest. T4 DNA ligase was able to perform this task, and the obtained ligation products were elongated by DNA polymerase. The effectiveness of ligation depends on the length of the random binding site of the mutagenic oligonucleotide, on its molar excess over the template-primer complex and on the position of the mismatching tri-nucleotide insert with respect to the joining site. The secondary structure of the DNA template close to the joining site also influences the ligation yield. Mismatching oligonucleotides, protected by a 3'-phosphate group, were joined to a nested set of megaprimers, the latter being obtained by a novel procedure called reversible chain termination, i.e., termination of the dsDNA synthesis with ddNTP followed by the subsequent removal of the incorporated ddNMP with exonuclease III. T7 sequenase 2.0 DNA polymerase elongated the ligation products after the 3'-phosphate protection group was removed with T4 polynucleotide kinase, resulting in the incorporation of a specific tri-nucleotide mismatch into dsDNA. This sequence of reactions serves as the basis for a novel scanning mutagenesis procedure.
Monitoring the Expression Pattern of 1300 Arabidopsis Genes under Drought and Cold Stresses by Using a Full-Length cDNA Microarray (2001)

Full-length cDNAs are essential for functional analysis of plant genes. Using the biotinylated CAP trapper method, we constructed full-length Arabidopsis cDNA libraries from plants in different conditions, such as drought-treated, cold-treated, or unstressed plants, and at various developmental stages from germination to mature seed. We prepared a cDNA microarray using approximately 1300 full-length Arabidopsis cDNAs to identify drought- and cold-inducible genes and target genes of DREB1A/CBF3, a transcription factor that controls stress-inducible gene expression. In total, 44 and 19 cDNAs for drought- and cold-inducible genes, respectively, were isolated, 30 and 10 of which were novel stress-inducible genes that have not been reported as drought- or cold-inducible genes previously. Twelve stress-inducible genes were identified as target stress-inducible genes of DREB1A, and six of them were novel. On the basis of RNA gel blot and microarray analyses, the six genes were identified as novel drought- and cold-inducible genes that are controlled by DREB1A. Eleven DREB1A target genes whose genomic sequences have been registered in the GenBank database contained the dehydration-responsive element (DRE) or DRE-related CCGAC core motif in their promoter regions. These results show that our full-length cDNA microarray is a useful material with which to analyze the expression pattern of Arabidopsis genes under drought and cold stresses, to identify target genes of stress-related transcription factors, and to identify potential cis-acting DNA elements by combining the expression data with the genomic sequence data.