gebhart/patrepeval huggingface dataset:
Rapid induction of mitogen-activated protein kinases by immune stimulatory CpG DNA. (1998)

Unmethylated CpG motifs in bacterial DNA or synthetic oligodeoxynucleotides (CpG DNA) rapidly activate B cells and monocyte-derived cells; however, the intracellular signaling pathways involved in this process are unclear. Here, we demonstrate that CpG DNA induces the activation of c-Jun NH2-terminal kinase and p38 but does not activate the extracellular receptor kinase in murine B and monocyte-like cell lines. CpG DNA also induces the phosphorylation of activating transcription factor-2, c-Jun, and mitogen-activated protein kinase (MAPK)-activated protein kinase 2 as well as the activation of activator protein-1 (AP-1) DNA binding. Inhibition of p38 led to the suppression of CpG DNA-induced AP-1 DNA-binding activity and cytokine production, indicating that the p38 pathway is required for mediating these immune stimulatory effects of CpG DNA. Chloroquine, an endosomal acidification inhibitor, selectively abolished CpG DNA-mediated MAPK activation. Our results indicate that CpG DNA activates the p38 and c-Jun NH2-terminal kinase MAPK and leads to the activation of AP-1 via a pathway which is sensitive to chloroquine.
Combination B7-Fc Fusion Protein Treatment and Treg Cell Depletion Therapy (2005)

The B7.1-Fc fusion protein seems to be an effective antitumor agent especially in combination with Treg depletion. Its potency in stimulating immune responses and its human origin suggest that clinical studies may be warranted in the future.
Applications of time-resolved light scattering measurements to photodynamic therapy dosimetry (1990)

Since biological response to photodynamic therapy (PDT) depends on the light fluence distribution and photosensitizer
concentration in the tissue, these two variables should ideally be measured noninvasively in individual
cases. This can be reduced to determining the optical absorption and transport scattering coefficients of the tissue
because, if these two parameters are known, the fluence distribution can be calculated and the photosensitizer concentration
can be deduced from its characteristic contribution to the absorption spectrum. The temporal spreading of
a picosecond laser pulse as it propagates through tissue carries infonnation about both the scattering and absorption
properties of the tissue. A mathematical model is presented which allows derivation of the interaction coefficients
from the pulse shape, and preliminary experiments are reported which demonstrate the potential of these techniques
in PDT dosimetry. Equivalent information can be obtained in the frequency domain by using modulated light sources
andmeasuring thephase and modulation of the detected light. Analytical expressions are developed for these observable
quantities in terms ofthe optical interaction coefficients. Particular auention is drawn to the potential oflow (less than
200 MHz) frequency measurements as these can be made with relatively simple instrumentation.
Treatment of hepatic metastasis of the colon26 adenocarcinoma with an alpha-galactosylceramide, KRN7000. (1998)

Colorectal liver metastasis is clinically a major problem. We examined the antitumor activity of KRN7000, an alpha-galactosylceramide, on mice with liver metastases of adenocarcinoma Colon26 cells. KRN7000 treatment, beginning 1 day after tumor inoculation (day 1), significantly inhibited tumor growth in the liver, and its potency was equal to that of interleukin 12. KRN7000 treatment from day 3 caused regression of established Colon26 nodules. KRN7000 administration resulted in a high percentage of cured mice that acquired tumor-specific immunity. In addition, it appeared that highly activated, liver-associated natural killer cells made the major contribution to the killing of Colon26 cells in the liver. These results suggest that KRN7000 may be useful for the treatment of colorectal liver metastasis.
Potential beneficial effects of butyrate in intestinal and extraintestinal diseases (2011)

The multiple beneficial effects on human health of the short-chain fatty acid butyrate, synthesized from non-absorbed carbohydrate by colonic microbiota, are well documented. At the intestinal level, butyrate plays a regulatory role on the transepithelial fluid transport, ameliorates mucosal inflammation and oxidative status, reinforces the epithelial defense barrier, and modulates visceral sensitivity and intestinal motility. In addition, a growing number of studies have stressed the role of butyrate in the prevention and inhibition of colorectal cancer. At the extraintestinal level, butyrate exerts potentially useful effects on many conditions, including hemoglobinopathies, genetic metabolic diseases, hypercholesterolemia, insulin resistance, and ischemic stroke. The mechanisms of action of butyrate are different; many of these are related to its potent regulatory effects on gene expression. These data suggest a wide spectrum of positive effects exerted by butyrate, with a high potential for a therapeutic use in human medicine.
Directional cDNA library construction assisted by the in vitro recombination reaction (2001)

We report here a new directional cDNA library construction method using an in vitro site-specific recombination reaction, based on the integrase-excisionase system of bacteriophage lambda. Preliminary experiments revealed that in vitro recombinational cloning (RC) provided important advantages over conventional ligation-assisted cloning: it eliminated restriction digestion for directional cloning, generated low levels of chimeric clones, reduced size bias and, in our hands, gave a higher cloning efficiency than conventional ligation reactions. In a cDNA cloning experiment using an in vitro synthesized long poly(A)(+) RNA (7.8 kb), the RC gave a higher full-length cDNA clone content and about 10 times more transformants than conventional ligation-assisted cloning. Furthermore, characterization of rat brain cDNA clones yielded by the RC method showed that the frequency of cDNA clones >2 kb having internal NotI sites was approximately 6%, whereas these cDNAs could not be cloned at all or could be isolated only in a truncated form by conventional methods. Taken together, these results indicate that the RC method makes it possible to prepare cDNA libraries better representing the entire population of cDNAs, without sacrificing the simplicity of current conventional ligation-assisted methods.
Cystic Fibrosis Transmembrane Conductance Regulator Is Required for Protein Kinase A Activation of an Outwardly Rectified Anion Channel Purified from Bovine Tracheal Epithelia (1995)

Our laboratory has developed a protocol for the isolation of a 140-kDa protein that forms an anion-selective channel when reconstituted into planar lipid bilayers. Polyclonal antibodies have been raised against the 38-kDa component of this purified protein. This channel has a linear current-voltage relationship and is not activated by protein kinase A (PKA) plus ATP. Using the same antibody and a modified purification protocol (eliminating the ion exchange chromatography steps), we isolated and reconstituted two other anion channels from tracheal membrane vesicles. In vitro phosphorylation of these isolated proteins by PKA and ATP revealed four bands migrating at 52, 85, 120, and 174 kDa. Immunoprecipitation experiments with anti-CFTR antibodies indicate that the 174-kDa phosphoprotein was CFTR. Upon incorporation of these isolated proteins into planar bilayers, an anion channel that exhibited a marked outward rectification in symmetrical Cl- solutions with a slope conductance of 82 pS at depolarizing voltages was observed. PKA and ATP increased channel activity but only from one side of the bilayer. However, channel activity was unaffected by addition of ATP alone from either side of the membrane. DIDS (100 microM) applied to the opposite side of the bilayer to which PKA and ATP act, blocked channel activity. A linear anion-selective channel with a conductance of 16 pS could be also resolved after inhibition of the outwardly rectified anion channel by DIDS in the presence of PKA and ATP. This small conductance channel was inhibited by 300 microM diphenylamine-2-carboxylic acid. Immunodepletion of the 174-kDa phosphoprotein from the preparation prevented activation of the 82-pS outwardly rectified anion channel by PKA and ATP. However, the PKA-dependent in vitro phosphorylation of the 52-, 85-, and 120-kDa phosphoproteins was unaffected by the absence of CFTR. Our results suggest a direct regulatory relationship between an outwardly rectified anion channel and CFTR.
Unusual Polymorphisms in Human Immunodeficiency Virus Type 1 Associated with Nonprogressive Infection (2000)

Factors accounting for long-term nonprogression may include infection with an attenuated strain of human immunodeficiency virus type 1 (HIV-1), genetic polymorphisms in the host, and virus-specific immune responses. In this study, we examined eight individuals with nonprogressing or slowly progressing HIV-1 infection, none of whom were homozygous for host-specific polymorphisms (CCR5-Delta32, CCR2-64I, and SDF-1-3'A) which have been associated with slower disease progression. HIV-1 was recovered from seven of the eight, and recovered virus was used for sequencing the full-length HIV-1 genome; full-length HIV-1 genome sequences from the eighth were determined following amplification of viral sequences directly from peripheral blood mononuclear cells (PBMC). Longitudinal studies of one individual with HIV-1 that consistently exhibited a slow/low growth phenotype revealed a single amino acid deletion in a conserved region of the gp41 transmembrane protein that was not seen in any of 131 envelope sequences in the Los Alamos HIV-1 sequence database. Genetic analysis also revealed that five of the eight individuals harbored HIV-1 with unusual 1- or 2-amino-acid deletions in the Gag sequence compared to subgroup B Gag consensus sequences. These deletions in Gag have either never been observed previously or are extremely rare in the database. Three individuals had deletions in Nef, and one had a 4-amino-acid insertion in Vpu. The unusual polymorphisms in Gag, Env, and Nef described here were also found in stored PBMC samples taken 3 to 11 years prior to, or in one case 4 years subsequent to, the time of sampling for the original sequencing. In all, seven of the eight individuals exhibited one or more unusual polymorphisms; a total of 13 unusual polymorphisms were documented in these seven individuals. These polymorphisms may have been present from the time of initial infection or may have appeared in response to immune surveillance or other selective pressures. Our results indicate that unusual, difficult-to-revert polymorphisms in HIV-1 can be found associated with slow progression or nonprogression in a majority of such cases.
Singlet oxygen reaction. IV. Photooxygenation of enamines involving a two-step cleavage of a 1,2-dioxetane intermediate (1975)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSinglet oxygen reaction. IV. Photooxygenation of enamines involving a two-step cleavage of a 1,2-dioxetane intermediateWataru Ando, Takeo Saiki, and Toshihiko MigitaCite this: J. Am. Chem. Soc. 1975, 97, 17, 5028–5029Publication Date (Print):August 1, 1975Publication History Published online1 May 2002Published inissue 1 August 1975https://pubs.acs.org/doi/10.1021/ja00850a055https://doi.org/10.1021/ja00850a055research-articleACS PublicationsRequest reuse permissionsArticle Views482Altmetric-Citations48LEARN 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
Advantages of Directional Hearing Aid Microphones Related to Room Acoustics (1991)

In this study, two types of hearing aids were used. Both aids had the same frequency characteristics for frontal sound, but one employed an omnidirectional microphone and the other a directional microphone. The frequency characteristics of both hearing aids were measured for five azimuths on KEMAR and in situ in 12 normal-hearing subjects. For these subjects we also determined the speech reception threshold (SRT) with background noise in two rooms with different reverberation times. The direction of the speech stimuli was always frontal; the direction of the noise was varied. Additionally, directional hearing was measured with short noise bursts from eight loudspeakers surrounding the subject. In the less reverberant room, sounds coming from behind were less amplified by the hearing aid with the directional microphone than by the one with the omnidirectional microphone. In this room the monaural SRT values were largely determined by the level of the background noise. For the directional hearing aids there was an extra binaural advantage which depended on the direction of the background noise. Only for low-frequency noise bursts was directional hearing better with directional hearing aids. In the more reverberant room, no distinct differences between the frequency characteristics of the two hearing aid types were measured. However, a systematic difference between monaural SRT values measured through the two hearing aids was found. This difference was independent of noise azimuth. In conclusion, hearing aid(s) with a directional microphone showed no disadvantages and clear advantages under specific conditions.
An insulin-like growth factor (IGF) binding protein enhances the biologic response to IGF-I. (1987)

The insulin-like growth factors IGF-I and IGF-II circulate in blood bound to carrier proteins. The higher molecular mass IGF-binding protein complex (150 kDa) is composed of subunits, and one subunit that forms this complex is growth hormone dependent. In addition, many cell types and tissues secrete another form of IGF binding protein that is not growth hormone dependent. Both forms of the IGF binding protein are believed to inactivate the IGFs and to function as delivery systems to tissues. This conclusion was based on studies that determined the effects of impure preparations of these binding proteins or that examined the effect of these proteins only on the insulin-like actions of the IGFs. We report here that a pure preparation of the extracellular form of the IGF binding protein (purified from human amniotic fluid) markedly potentiated replication of several cell types in response to human IGF-I. Secondary cultures of human, mouse, and chicken embryo fibroblasts as well as porcine aortic smooth muscle cells showed marked enhancement of their DNA synthesis response (2.8- to 4.4-fold increases) to IGF-I in the presence of this protein. These responses were synergistic since the sum of the responses to either IGF-I or to the binding protein alone was between 8 and 17% of the increase obtained in cultures exposed to both peptides. The binding protein not only potentiated the DNA synthesis response but also enhanced the increase in cell number in response to IGF-I. This stimulation is specific for growth factors that bind to the binding protein since incubation with insulin, which binds to the type I IGF receptor but not to the binding protein, did not result in potentiation of this response. We conclude that a form of IGF binding protein that is present in extracellular fluids and is secreted by many types of cells can markedly potentiate the cellular response to IGF-I.
SR protein kinases: the splice of life (1999)

The eukaryotic genome codes for most of its proteins though discontinuous coding sequences called exons, which are separated by noncoding sequences known as introns. Following transcription of a gene, these exons must be spliced precisely, removing the intervening introns, to form meaningful mature messenger RNAs (mRNA) that are transported to the cytoplasm and translated by the ribosomal machinery. To add yet another level of complexity, a process known as alternative splicing exists, whereby a single pre-mRNA can give rise to two or more mature mRNAs depending on the combination of exons spliced together. Alternative splicing of pre-mRNAs is emerging as an important mechanism for gene regulation in many organisms. The classic example of splicing as a regulator of genetic information during a developmental process is sex determination in Drosophila. The now well-characterized cascade of sex-specific alternative splicing events demonstrates nicely how the control of splice site selection during pre-mRNA processing can have a profound effect on the development of an organism. The factors involved in pre-mRNA splicing and alternative splice site selection have been the subject of active study in recent years. Emerging from these studies is a picture of regulation based on protein-protein, protein-RNA, and RNA-RNA interactions. How the interaction of the various splicing constituents is controlled, however, is still poorly understood. One of the mechanisms of regulation that has received attention recently is that of posttranslational phosphorylation. In the following article, we cite the evidence for a role of phosphorylation in constitutive and alternative splicing and discuss some of the recent information on the biochemistry and biology of the enzymes involved.
Congenital Cholestatic Syndromes: What Happens When Children Grow Up? (2007)

Although advances in the management of children with congenital cholestasis have enabled many to survive into adulthood with their native livers, even the most common of these conditions remains rare in adult hepatology practice. Among four congenital cholestatic syndromes (biliary atresia, Alagille syndrome, Caroli disease and congenital hepatic fibrosis, and progressive familial intrahepatic cholestasis), the published data on outcomes of the syndromes into adulthood suggest that a spectrum of severity of liver disease can be expected, from cirrhosis (almost universal in adults with biliary atresia who have not required liver transplantation) to mild and subclinical (eg, in the previously undiagnosed affected parent of an infant with Alagille syndrome). Complications associated with portal hypertension and nutritional deficiencies are common, and other associated features of the cholestatic syndrome may require appropriate attention, such as congenital heart disease in Alagille syndrome. Indications for liver transplantation include synthetic failure, progressive encephalopathy, intractable pruritus, recurrent biliary sepsis and recurrent complications of portal hypertension. Improved understanding of biliary physiology will hopefully translate into improved therapy for children and adults with cholestasis.
A gene encoding an intestinal-enriched member of the Kruppel-like factor family expressed in intestinal epithelial cells (1999)

The Krüppel-like factors make up a multigene family of transcription factors that have discrete patterns of expression, implying they play important biological roles in the tissues in which they are expressed. We have identified and characterized the cDNA for a novel murine transcription factor that is an additional member of the Krüppel-like family of transcription factors, named intestinal-enriched Krüppel-like factor (IKLF). This gene appears to be a homolog of the human BTEB-2 gene, although it exhibits a different pattern of tissue expression and the translated product is larger. IKLF is expressed in a limited number of tissues; the highest levels of IKLF expression are found in the digestive tract. IKLF shows temporal changes in expression during embryogenesis indicating that this gene is developmentally regulated. In addition, IKLF expression is limited to the epithelial lining of the intestine and is localized primarily to the base of the crypts in the adult intestine. The IKLF cDNA encodes for a 446 amino acid protein and is able to transactivate by binding specific DNA elements that are also recognized by other members of the Krüppel-like family. In addition, mutations in the activation domain attenuate the ability of this protein to function as a transcription factor. Collectively, these findings show that we have identified a transcription factor that is expressed predominantly in the epithelial crypt cells of the gastrointestinal tract and is a member of the Krüppel-like family of transcription factors.
Deficiency of c-kit+ cells in patients with a myopathic form of chronic idiopathic intestinal pseudo-obstruction. (1997)

The failure of intestinal movement in patients with CIIP, at least in a subpopulation, might be related to a deficiency of c-kit+ cells, probably ICCs.
A 36-Pixel Tunnel Junction Soft X-Ray Spectrometer for Scintillator Material Science (2007)

We have built a 36-pixel superconducting tunnel junction (STJ) spectrometer for high-resolution soft X-ray spectroscopy at the synchrotron. It has an energy resolution between ~10 and ~20 eV FWHM for X-ray energies below ~1 keV, and can be operated at maximum total count rates of ~10 <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">6</sup> counts/s. For increased sensitivity, we have modified the detector cold finger the so that the array now subtends a solid angle of Omega/4pi ap0.1%. The spectrometer is currently used at the Advanced Light Source synchrotron for speciation measurements of dilute samples by fluorescence-detected X-ray absorption spectroscopy. We present measurements of the oxidation state of dilute cerium activators in novel scintillator materials, determine the Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">3+</sup> /Ce <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">4+</sup> ratio, and discuss the sensitivity of the instrument for quantitative speciation measurements.
Ramped-Amplitude Cross Polarization in Magic-Angle-Spinning NMR (1994)

The Hartmann-Hahn matching profile in CP-MAS NMR shows a strong mismatch dependence if the MAS frequency is on the order of the dipolar couplings in the sample. Under these conditions, the profile breaks down into a series of narrow matching bands separated by the spinning speed, and it becomes difficult to establish and maintain an efficient matching condition. Variable-amplitude CP (VACP), as introduced previously (Peersen et al., J. Magn. Reson. A104, 334, 1993), has been proven to be effective for restoring flat profiles at high spinning speeds. Here, a refined implementation of VACP using a ramped-amplitude cross-polarization sequence (RAMP-CP) is described. The order of the amplitude modulation is shown to be of importance for the cross-polarization process. The new pulse sequence with a linear amplitude ramp is not only easier to set up but also improves the performance of the variable-amplitude experiment in that it produces flat profiles over a wider range of matching conditions even with short total contact times. An increase in signal intensity is obtained compared to both con ventional CP and the originally proposed VACP sequence.