gebhart/patrepeval huggingface dataset:
Immunomodulatory effects of IL-12 on allergic lung inflammation depend on timing of doses (1996)

We investigated the effects of IL-12 on a murine model of allergic lung inflammation. Administration of IL-12 was timed to interfere with either allergic sensitization (early dosage) or the hypersensitivity inflammatory response in the lung (late dosage), or both (early and late dosages). Comparisons of IL-12- and PBS-treated animals within each treatment group revealed several noticeable effects of IL-12. Early dosage, and the combination of early and late dosages, strikingly decreased ragweed-specific serum IgE, tracheal ring reactivity to acetylcholine, and BAL eosinophilia following allergen challenge. In contrast, late dosage had no effect on IgE levels and only a minimal effect on tracheal ring reactivity, but had a modest effect on recruitment of eosinophils. Early dosage down-regulated IL-5 and IL-10, but did not alter IL-4 or IFN-gamma expression. Late dosage down-regulated IL-5, up-regulated IL-10 and IFN-gamma, but did not change IL-4 expression. The combination of early and late dosage down-regulated IL-4, IL-5, and IL-10 expression, but increased IFN-gamma expression and production in the BAL cells and fluids. Taken together, these results indicate that IL-12 has potent immunomodulatory effects on allergic lung inflammation that depend on the timing of IL-12 administration relative to allergic sensitization and allergen challenge.
Experimental verification of epsilon-near-zero plasmon polariton modes in degenerately doped semiconductor nanolayers (2016)

We investigate optical polariton modes supported by subwavelength-thick degenerately doped semiconductor nanolayers (e.g. indium tin oxide) on glass in the epsilon-near-zero (ENZ) regime. The dispersions of the radiative (R, on the left of the light line) and non-radiative (NR, on the right of the light line) ENZ polariton modes are experimentally measured and theoretically analyzed through the transfer matrix method and the complex-frequency/real-wavenumber analysis, which are in remarkable agreement. We observe directional near-perfect absorption using the Kretschmann geometry for incidence conditions close to the NR-ENZ polariton mode dispersion. Along with field enhancement, this provides us with an unexplored pathway to enhance nonlinear optical processes and to open up directions for ultrafast, tunable thermal emission.
Multiplexed Quantification of Nucleic Acids with Large Dynamic Range Using Multivolume Digital RT-PCR on a Rotational SlipChip Tested with HIV and Hepatitis C Viral Load (2011)

In this paper, we are working toward a problem of great importance to global health: determination of viral HIV and hepatitis C (HCV) loads under point-of-care and resource limited settings. While antiretroviral treatments are becoming widely available, viral load must be evaluated at regular intervals to prevent the spread of drug resistance and requires a quantitative measurement of RNA concentration over a wide dynamic range (from 50 up to 10(6) molecules/mL for HIV and up to 10(8) molecules/mL for HCV). "Digital" single molecule measurements are attractive for quantification, but the dynamic range of such systems is typically limited or requires excessive numbers of compartments. Here we designed and tested two microfluidic rotational SlipChips to perform multivolume digital RT-PCR (MV digital RT-PCR) experiments with large and tunable dynamic range. These designs were characterized using synthetic control RNA and validated with HIV viral RNA and HCV control viral RNA. The first design contained 160 wells of each of four volumes (125 nL, 25 nL, 5 nL, and 1 nL) to achieve a dynamic range of 5.2 × 10(2) to 4.0 × 10(6) molecules/mL at 3-fold resolution. The second design tested the flexibility of this approach, and further expanded it to allow for multiplexing while maintaining a large dynamic range by adding additional wells with volumes of 0.2 nL and 625 nL and dividing the SlipChip into five regions to analyze five samples each at a dynamic range of 1.8 × 10(3) to 1.2 × 10(7) molecules/mL at 3-fold resolution. No evidence of cross-contamination was observed. The multiplexed SlipChip can be used to analyze a single sample at a dynamic range of 1.7 × 10(2) to 2.0 × 10(7) molecules/mL at 3-fold resolution with limit of detection of 40 molecules/mL. HIV viral RNA purified from clinical samples were tested on the SlipChip, and viral load results were self-consistent and in good agreement with results determined using the Roche COBAS AmpliPrep/COBAS TaqMan HIV-1 Test. With further validation, this SlipChip should become useful to precisely quantify viral HIV and HCV RNA for high-performance diagnostics in resource-limited settings. These microfluidic designs should also be valuable for other diagnostic and research applications, including detecting rare cells and rare mutations, prenatal diagnostics, monitoring residual disease, and quantifying copy number variation and gene expression patterns. The theory for the design and analysis of multivolume digital PCR experiments is presented in other work by Kreutz et al.
TRANSPORT OF LIGHT IN TISSUE IN PHOTODYNAMIC THERAPY (1987)

Abstract The dose rate in photodynamic therapy is proportional to the energy fluence rate and the concentration of the photosensitizer. Calculations of the energy fluence rate have been performed in slab, cylindrical and spherical geometries with the discrete ordinates transport method and diffusion theory. The attentuation of the energy fluence rate is least in slab geometry and greatest in spherical geometry. Violet (405 nm) light is attenuated much more rapidly than red (630 nm) light. Small tissue dimensions or narrow beam irradiation further decrease the energy fluence rate with radius and depth. Anisotropic scattering increases the energy fluence rate at large depths, but decreases it near the source. Measurements of the absolute energy fluence rate vs depth in a mouse tumor model exhibit an order of magnitude attenuation through the skin and a 3 mm thick tumor. Calculations of the energy fluence rate of the DHE fluorescence have been carried out to guide measurement of the concentration. Violet light excitation is much more efficient than red light excitation.
Computational definition of sequence motifs governing constitutive exon splicing (2004)

We have searched for sequence motifs that contribute to the recognition of human pre-mRNA splice sites by comparing the frequency of 8-mers in internal noncoding exons versus unspliced pseudo exons and 5' untranslated regions (5' untranslated regions [UTRs]) of transcripts of intronless genes. This type of comparison avoids the isolation of sequences that are distinguished by their protein-coding information. We classified sequence families comprising 2069 putative exonic enhancers and 974 putative exonic silencers. Representatives of each class functioned as enhancers or silencers when inserted into a test exon and assayed in transfected mammalian cells. As a class, the enhancer sequencers were more prevalent and the silencer elements less prevalent in all exons compared with introns. A survey of 58 reported exonic splicing mutations showed good agreement between the splicing phenotype and the effect of the mutation on the motifs defined here. The large number of effective sequences implied by these results suggests that sequences that influence splicing may be very abundant in pre-mRNA.
Affinity labeling of the polyphosphate binding site of hemoglobin (1972)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTAffinity labeling of the polyphosphate binding site of hemoglobinRuth E. Benesch, Reinhhold Benesch, Robert D. Renthal, and Nobuji MaedaCite this: Biochemistry 1972, 11, 19, 3576–3582Publication Date (Print):September 12, 1972Publication History Published online1 May 2002Published inissue 12 September 1972https://pubs.acs.org/doi/10.1021/bi00769a013https://doi.org/10.1021/bi00769a013research-articleACS PublicationsRequest reuse permissionsArticle Views246Altmetric-Citations242LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
Topical maxacalcitol for the treatment of psoriasis vulgaris: a placebo-controlled, double-blind, dose-finding study with active comparator (1999)

1alpha, 25-Dihydroxy-22-oxacalcitriol (maxacalcitol) is a vitamin D3 analogue which displays approximately 10 times greater efficacy at suppressing keratinocyte proliferation in vitro than calcipotriol and tacalcitol. To determine clinical efficacy, a phase II double-blind, randomized, left vs. right, concentration-response study was performed with once-daily topical maxacalcitol in patients with mild to moderate chronic plaque psoriasis. Primary efficacy parameters were psoriasis severity index (PSI) based on sum of scores for erythema, scaling and induration and investigators' overall assessment of patients' response to therapy at 8 weeks of treatment. One hundred and forty-four patients participated. All concentrations of maxacalcitol ointment (6, 12.5, 25 and 50 microg/g) were significantly more effective at reducing PSI than placebo (P < 0.01), with greatest effect noted for maxacalcitol 25 microg/g. Calcipotriol ointment 50 microg/g once daily as active comparator had a similar effect. Marked improvement or clearance of psoriasis was greatest for maxacalcitol 25 microg/g (55% of subjects) which compared favourably with calcipotriol (46%). Improvement continued throughout the study period, with no plateau at week 8. Investigators' and patients' side preference (secondary efficacy parameters) rated maxacalcitol more effective than placebo and 25 microg/g maxacalcitol better than calcipotriol (P < 0.05 for investigators' assessment). Twelve patients withdrew from the study due to adverse events, of which four were judged to be due to study medication. This study indicates that once-daily maxacalcitol ointment is effective in the management of plaque psoriasis, with greatest effect noted at 25 microg/g. As no response plateau was noted at 8 weeks, these data suggest that further benefit might be obtained if maxacalcitol ointment were applied for longer. Finally, investigators' overall assessment and side preference suggest that maxacalcitol 25 microg/g may be more effective than once-daily calcipotriol.
Delineation, Functional Validation, and Bioinformatic Evaluation of Gene Expression in Thyroid Follicular Carcinomas with the PAX8-PPARG Translocation (2006)

A subset of follicular thyroid carcinomas contains a balanced translocation, t(2;3)(q13;p25), that results in fusion of the paired box gene 8 (PAX8) and peroxisome proliferator-activated receptor gamma (PPARG) genes with concomitant expression of a PAX8-PPARgamma fusion protein, PPFP. PPFP is thought to contribute to neoplasia through a mechanism in which it acts as a dominant-negative inhibitor of wild-type PPARgamma. To better understand this type of follicular carcinoma, we generated global gene expression profiles using DNA microarrays of a cohort of follicular carcinomas along with other common thyroid tumors and used the data to derive a gene expression profile characteristic of PPFP-positive tumors. Transient transfection assays using promoters of four genes whose expression was highly associated with the translocation showed that each can be activated by PPFP. PPFP had unique transcriptional activities when compared with PAX8 or PPARgamma, although it had the potential to function in ways qualitatively similar to PAX8 or PPARgamma depending on the promoter and cellular environment. Bioinformatics analyses revealed that genes with increased expression in PPFP-positive follicular carcinomas include known PPAR target genes; genes involved in fatty acid, amino acid, and carbohydrate metabolism; micro-RNA target genes; and genes on chromosome 3p. These results have implications for the neoplastic mechanism of these follicular carcinomas.
Selective breeding for diet-induced obesity and resistance in Sprague-Dawley rats (1997)

In outbred Sprague-Dawley rats, about one-half develop diet-induced obesity (DIO) on a diet relatively high in fat and energy (HE diet). The rest are diet resistant (DR), gaining weight and fat at the same rate as chow-fed controls. Here we selectively bred for high (DIO) and low (DR) weight gainers after 2 wk on HE diet. By the F5 generation, both male and female inbred DIO rats gained &gt; 90% more weight than inbred DR rats on HE diets. Even on low-fat chow diet, DIO males were 31% and females were 22% heavier than their respective DR rats. Full metabolic characterization in male rats showed that weight-matched, chow-fed DIO-prone rats had similar energy intakes and feed efficiency [body weight (kg0.75)/energy intake (kcal)] but 44% more carcass fat than comparable DR-prone rats. Their basal plasma insulin and glucose levels in the fed state were 70 and 14% higher, respectively. But, when fasted, DIO-prone oral glucose tolerance results were comparable to DR-prone rats. Chow-fed DIO-prone males also had 42% greater 24-h urine norepinephrine levels than DR-prone males. During 2 wk on HE diet, DIO rats ate 25% more, gained 115% more weight, had 36% more carcass fat, and were 42% more feed efficient than comparable DR rats. Fasted HE diet-fed DIO rats developed frank glucose intolerance during a glucose tolerance test with 55 and 158% greater insulin and glucose areas under the curve, respectively. Thus the DIO and DR traits in the outbred Sprague-Dawley population appear to be due to a polygenic pattern of inheritance.
A comparative study of mucin-like carcinoma-associated antigen (MCA), CA 125, CA 19-9 and CEA in patients with ovarian cancer. (1989)

A mucin-like carcinoma associated antigen (MCA), which is recognized by the monoclonal antibody b-12, was found to be elevated in sera of breast cancer patients. Since an immunohistochemical reaction of the monoclonal antibody b-12 was found in epithelial tumors of the ovary we investigated MCA serum levels in 50 patients with ovarian cancer (mean age 59 years, range 31-81 years). In addition, CA 125, CA 19-9 and CEA were determined to compare sensitivity, specificity and the predictive value of the positive test of each parameter used in this study. Blood samples were obtained in 20 patients with progressive disease and in 30 patients during disease free intervals. The MCA serum levels of patients with progressive ovarian cancer (mean +/- SD: 14.7 +/- 14.6 U/ml) did not differ significantly from those of patients in remission (mean +/- SD: 8.2 +/- 5.3 U/ml) or from values of a healthy control group (mean +/- SD: 7.7 +/- 3.8 U/ml, n = 70). Women with progressive disease displayed significantly higher CA 125 (p less than 0.0001) and CEA (p less than 0.0063) serum levels than patients in remission. No significant difference was found for CA 19-9 in patients with ovarian cancer, irrespective of the clinical status. Considering marker surge and tumor progression, the highest sensitivity was found for CA 125 (75%). Sensitivities of the other markers were significantly lower and reached only 25-35%. The predictive value of elevated marker levels as well as specificity of the marker substances were similar. Sensitivity could be extended to 90% if elevation of CA 125, CA 19-9, CEA and MCA were taken into consideration, however specificity was lowered by using this marker combination.
Biomimetic cavity-based metal complexes (2014)

The design of biomimetic complexes for the modeling of metallo-enzyme active sites is a fruitful strategy for obtaining fundamental information and a better understanding of the molecular mechanisms at work in Nature's chemistry. The classical strategy for modeling metallo-sites relies on the synthesis of metal complexes with polydentate ligands that mimic the coordination environment encountered in the natural systems. However, it is well recognized that metal ion embedment in the proteic cavity has key roles not only in the recognition events but also in generating transient species and directing their reactivity. Hence, this review focuses on an important aspect common to enzymes, which is the presence of a pocket surrounding the metal ion reactive sites. Through selected examples, the following points are stressed: (i) the design of biomimetic cavity-based complexes, (ii) their corresponding host-guest chemistry, with a special focus on problems related to orientation and exchange mechanisms of the ligand within the host, (iii) cavity effects on the metal ion binding properties, including 1st, 2nd, and 3rd coordination spheres and hydrophobic effects and finally (iv) the impact these factors have on the reactivity of embedded metal ions. Important perspectives lie in the use of this knowledge for the development of selective and sensitive probes, new reactions, and green and efficient catalysts with bio-inspired systems.
MIMO systems with antenna selection (2004)

Multiple-input-multiple-output (MIMO) wireless systems are those that have multiple antenna elements at both the transmitter and receiver. They were first investigated by computer simulations in the 1980s. Since that time, interest in MIMO systems has exploded. They are now being used for third-generation cellular systems (W-CDMA) and are discussed for future high-performance modes of the highly successful IEEE 802.11 standard for wireless local area networks. MIMO-related topics also occupy a considerable part of today's academic communications research. The multiple antennas in MIMO systems can be exploited in two different ways. One is the creation of a highly effective antenna diversity system; the other is the use of the multiple antennas for the transmission of several parallel data streams to increase the capacity of the system. This article presented an overview of MIMO systems with antenna selection. The transmitter, the receiver, or both use only the signals from a subset of the available antennas. This allows considerable reductions in the hardware expense.
First-Generation RCA Direct Broadcast Satellites (1985)

In October 1982, the Satellite Television Corporation (STC), a subsidiary of the Communications Satellite Corporation (Comsat), contracted with RCA Astro-Electronics to design, develop, and manufacture the first direct broadcast satellite for use in the United States. The contract is for two spacecraft with an early 1986 launch from either Kourou, Guiana, or Kennedy Space Center, Florida. The program is on schedule with all designs finalized, component qualification virtually complete, and the first spacecraft undergoing integration. Although the system will be implemented in phases, some recent design changes will permit the two collocated satellites to deliver six DBS channels to the entire conterminous United States (CONUS), three channels per satellite. Orbital location will be 110° W longitude, which is one of the eight orbit locations specified for the United States at the Regional Area Radio Conference (RARC) in 1983. Each channel is designed to generate 220 W of RF power in the 12.2-12.7 GHz band at the beginning of life; an allowance is made for TWTA efficiency degradation with life to provide 200 W of RF power at the end of life. The three channels per spacecraft are provided whenever the spacecraft is illuminated by the sun, with no requirement for eclipse operation. Each spacecraft has the capability to transmit in either of two different coverage configurations: it can provide coverage to CONUS or to half-CONUS at an increase in e.i.r.p. of approximately 3 dB. This provides additional margin should STC need the higher e.i.r.p. in the future or provides for a flexible time-zone coverage of the United States.
The Saccharomyces cerevisiae Msh2 protein specifically binds to duplex oligonucleotides containing mismatched DNA base pairs and insertions. (1995)

The yeast Saccharomyces cerevisiae encodes four proteins, Msh1, Msh2, Msh3, Msh4, that show strong amino acid sequence similarity to MutS, a central component of the bacterial mutHLS mismatch repair system. MutS has been shown to recognize base pair mismatches in DNA in vitro. Previous studies have suggested that Msh2 is the major mismatch recognition protein in yeast. In this study, the 109-kD Msh2 polypeptide was overexpressed and purified to analyze its DNA-binding properties. This analysis demonstrated that Msh2 can bind selectively to duplex oligonucleotide substrates containing a G/T mismatch, 1- to 14-nucleotide insertion mismatches, and palindromic (12- to 14-nucleotide) insertion mismatches. A general trend was that the affinity of Msh2 for substrate was proportional to the size of the insertion mispair present (+14 PAL, +12 PAL > +14 > +8 > GT, +6, +4, +2, +1). Kinetic studies indicated that the specificity of Msh2 to mismatch substrates was a function of its ability to form stable complexes with mispair-containing duplex DNAs. These complexes decayed more slowly than Msh2 complexes formed with homoduplex DNA.
Primary structure of bovine vitamin K-dependent protein S. (1986)

Protein S is a vitamin K-dependent plasma protein that functions as a cofactor to activated protein C in the inactivation of coagulation factors Va and VIIIa. The nucleotide sequence of a full-length cDNA clone, obtained from a bovine liver library, was determined and the amino acid sequence was deduced. In addition, 95% of the structure was determined by protein sequencing. Protein S consists of 634 amino acids in a single polypeptide chain and has one asparagine-linked carbohydrate side chain. The cDNA sequence showed that the protein has a leader sequence, 41 amino acid residues long. The amino-terminal part of the molecule containing gamma-carboxyglutamic acid is followed by a region, residues 42-75, with two peptide bonds that are very sensitive to cleavage by thrombin. Residues 76-244 have four cysteinerich repeat sequences, each about 40 residues long, that are homologous to the precursor of mouse epidermal growth factor. In contrast to the other vitamin K-dependent plasma proteins, the carboxyl-terminal part of protein S is not homologous to the serine proteases.