gebhart/patrepeval huggingface dataset:
Creating and Maintaining the Gastrointestinal Ecosystem: What We Know and Need To Know from Gnotobiology (1998)

Studying the cross talk between nonpathogenic organisms and their mammalian hosts represents an experimental challenge because these interactions are typically subtle and the microbial societies that associate with mammalian hosts are very complex and dynamic. A large, functionally stable, climax community of microbes is maintained in the murine and human gastrointestinal tracts. This open ecosystem exhibits not only regional differences in the composition of its microbiota but also regional differences in the differentiation programs of its epithelial cells and in the spatial distribution of its component immune cells. A key experimental strategy for determining whether "nonpathogenic" microorganisms actively create their own regional habitats in this ecosystem is to define cellular function in germ-free animals and then evaluate the effects of adding single or several microbial species. This review focuses on how gnotobiotics-the study of germ-free animals-has been and needs to be used to examine how the gastrointestinal ecosystem is created and maintained. Areas discussed include the generation of simplified ecosystems by using genetically manipulatable microbes and hosts to determine whether components of the microbiota actively regulate epithelial differentiation to create niches for themselves and for other organisms; the ways in which gnotobiology can help reveal collaborative interactions among the microbiota, epithelium, and mucosal immune system; and the ways in which gnotobiology is and will be useful for identifying host and microbial factors that define the continuum between nonpathogenic and pathogenic. A series of tests of microbial contributions to several pathologic states, using germ-free and ex-germ-free mice, are proposed.
[Cytokeratin expression in human junctional epithelium, oral epithelium and sulcular epithelium]. (2005)

JE is an unique non-differentiated stratified epithelium different from OE and SE. CK19 would be a histological marker and CK10/13, 16 would be the cellular markers to differentiate JE from OE and SE.
The human erythrocyte contains two forms of phosphatidylinositol-4-phosphate 5-kinase which are differentially active toward membranes. (1990)

A human erythrocyte cytosolic phosphatidylinositol-4-phosphate 5-kinase (PIP kinase) and a membrane-bound PIP kinase have been purified by phosphocellulose chromatography. Fractionation of the membrane-bound PIP kinase activities by phosphocellulose separated activity into two peaks, which eluted at 0.6 M NaCl (type I PIP kinase) and 1.0 M NaCl (type II PIP kinase). The cytosolic PIP kinase and the membrane-bound type II PIP kinase are 53 kDa by sodium dodecyl sulfate-polyacrylamide gel electrophoresis, have indistinguishable 125I-peptide maps, and are immunochemically indistinguishable, suggesting that they are sequence identical. Antibodies raised to the cytosolic PIP kinase inhibit activity of both the membrane-bound type II and the cytosolic PIP kinases. The type I PIP kinase appears to be distinct from the cytosolic and membrane-bound type II PIP kinase; it is not immunocross-reactive, and antibodies toward type II PIP kinases do not inhibit type I PIP kinase. Further, membrane-bound type II PIP kinase can be removed from type I PIP kinase without loss of activity. Functional characterization of the PIP kinases demonstrates that the type I kinase has a 10-fold lower Km for PIP and a 5-fold higher Km for ATP compared with the type II enzymes. The type I and type II (membrane-bound or cytosolic) PIP kinases are modulated differentially by spermine and heparin. Finally, the type I PIP kinase phosphorylates intrinsic PIP on isolated erythrocyte membranes, whereas the type II PIP kinases have no activity toward native membranes.
Synthese und Eigenschaften einiger tert‐Alkylmalonsäurederivate (1981)

Abstract Aus den Alkylidenmalonsäurederivaten 1–8 wurden durch 1,4‐Addition von Grignard‐Reagenzien die tert ‐Alkylmalonsäurederivate 9–18 hergestellt. Aus den Estern 9–17 wurden die Säuren 19–26 und aus diesen die Säurechloride 27–34 gewonnen. Bromierungen lieferten die Bromsäuren 35–36 , das bromierte Säurebromid 43 , das Bromnitril 44 und die bromierten Säurechloride 37–42 . Die Trimethylsilylester 50–52 , die Bis(2‐bromethyl)ester 53–54 , der Ethylester 14 und der tert ‐Butylester 16 wurden über die mit Lithium(cyclohexyl)isopropylamid hergestellten Esterenolate bromiert, wobei die Bromester 45–46 rein erhalten wurden. — Versuche zur Entalkylierung von Malonestern mit Chlortrimethylsilan/Natriumiodid wurden durchgeführt.
The Max Transcription Factor Network: Involvement of Mad in Differentiation and an Approach to Identification of Target Genes (1994)

The small bHLHZip protein, Max, was originally identified through its interaction with Myc family proteins and appears to be an obligate partner for Myc function. Max has now been found to interact with at least two other proteins, Mad and Mxi1. These also belong to the bHLHZip class but are otherwise unrelated to Myc. Mad has been shown to abrogate the positive transcriptional activity of Myc and to inhibit Myc in co-transformation assays. This suggests that Mad may antagonize Myc function. Mad is rapidly induced upon differentiation, a time when Myc is frequently down-regulated. We show here evidence for Mad expression upon differentiation of myeloblasts, monoblasts, and keratinocytes. Mad:Max complexes are detected during differentiation and appear to replace the Myc:Max complexes present in proliferating cell populations. Since these complexes appear to form even in the presence of Myc, there may exist mechanisms that act to inhibit Myc:Max, or to promote Mad:Max, complex formation. We speculate that Max complex switching causes a change in the transcriptional activity of groups of target genes. Mad is not induced in all differentiating cell types, suggesting that other, possibly tissue-restricted, proteins might act in similar switch mechanisms to effect changes in transcriptional programs. We have also developed an approach to identification of the gene targets for Myc:Max complexes. By employing an immunoisolation procedure, we have begun characterization of several clones whose expression levels correlate with those of c-myc. Further identification of Myc-regulated genes may allow us to determine the molecular mechanism by which Myc governs cell proliferation and differentiation.
Urokinase-type plasminogen activator is expressed in stromal cells and its receptor in cancer cells at invasive foci in human colon adenocarcinomas. (1991)

In this study in situ hybridization methods were used to examine biopsy samples from 13 adenocarcinomas of the colon for the presence of mRNA for the urokinase-type plasminogen activator (u-PA) and its specific cell-surface receptor (u-PAR). In all cases, u-PA mRNA was present in fibroblastlike cells in the stroma adjacent to the invasive tumor nodules. Urokinase-type plasminogen activator mRNA was not detected in the malignant cells. All specimens also contained u-PAR mRNA in cells located at the tumoral-stromal interface of invasive foci, but in contrast at least some of these cells were in all but one case identified as being of malignant origin. Stromal cells, probably tumor-infiltrating macrophages and neutrophils, also were positive in these areas. These results support the view that components of the plasminogen activation system may act to influence proteolytic events occurring at the interface between stroma and malignant cells in adenocarcinomas of the colon in humans.
A review of the evidence for carbamazepine and oxcarbazepine in the treatment of bipolar disorder (2004)

Bipolar disorder is a recurrent lifelong condition associated with significant morbidity and mortality. The main goals of treatment are the acute management of manic/depressive episodes and the prevention of recurrence. Mood stabilizers are the basis of most treatment regimens. Although lithium is the classical mood stabilizer, dissatisfaction with its efficacy and tolerability has led to increased use of other mood- stabilizing agents, including anticonvulsants. Newer anticonvulsants such as oxcarbazepine may offer improved tolerability and fewer drug-drug interactions compared to older drugs like carbamazepine. A search of the literature shows that data from controlled clinical studies support the efficacy of carbamazepine in treating acute mania and as maintenance therapy. In addition, a growing body of data for oxcarbazepine suggests that this newer agent may have a similar efficacy profile to carbamazepine, with improved tolerability. This review presents a balanced selection of the key studies on carbamazepine and oxcarbazepine in bipolar disorder.
The American Cancer Society Cancer Prevention Study II Nutrition Cohort (2002)

This new cohort of both men and women promises to be particularly valuable for the study of cancer occurrence, mortality, and survival as they relate to obesity and weight change, physical activity at various points in life, vitamin supplement use, exogenous hormone use, other medications (such as aspirin and nonsteroidal anti-inflammatory drugs) and cancer screening modalities.
Bifunctional Ligands that Target Cells Displaying the αvβ3 Integrin (2006)

Strategies to eliminate tumor cells have long been sought. We envisioned that a small molecule could be used to decorate the offending cells with immunogenic carbohydrates and evoke an immune response. To this end, we describe the synthesis of bifunctional ligands possessing two functional motifs: one binds a cell-surface protein and the other binds a naturally occurring human antibody. Our conjugates combine an RGD-based peptidomimetic, to target cells displaying the alpha v beta3 integrin, with the carbohydrate antigen galactosyl-alpha(1-3)galactose [Galalpha(1-3)Gal or alpha-Gal]. To generate such bifunctional ligands, we designed and synthesized RGD mimetics 1 b and 2 c, which possess a free amino group for modification. These compounds were used to generate bifunctional derivatives 1 c and 2 d, with dimethyl squarate serving as the linchpin; thus, our synthetic approach is modular. To evaluate the binding of our peptidomimetics to the target alpha v beta3-displaying cells, we implemented a cell-adhesion assay. Results from this assay indicate that the designed, small-molecule ligands inhibit alpha v beta3-dependent cell adhesion. Additionally, our most effective bifunctional ligand exhibits a high degree of selectivity (4000-fold) for alpha v beta3 over the related alpha v beta5 integrin, a result that augurs its utility in specific cell targeting. Finally, we demonstrate that the bifunctional ligands can bind to alpha v beta3-positive cells and recruit human anti-Gal antibodies. These results indicate that both the integrin-binding and the anti-Gal-binding moieties can act simultaneously. Bifunctional conjugates of this type can facilitate the development of new methods for targeting cancer cells by exploiting endogenous antibodies. We anticipate that our modifiable alpha v beta3-binding ligands will be valuable in a variety of applications, including drug delivery and tumor targeting.
Measuring Cognitive Distraction in the Automobile II: Assessing In-Vehicle Voice-Based InteractiveTechnologies (2014)

The goal of the current research was to measure and understand cognitive distraction stemming from voice-based technologies in the vehicle. Three controlled experiments evaluated 1) a baseline single-task condition, 2) issuing simple voice-based car commands, 3) listening to e-mail/text messages read by a “natural” pre-recorded human voice, 4) listening to e-mail/text messages read by a “synthetic” computerized text-to-speech system, 5) listening and composing replies to e-mail/text messages read by a “natural” voice, 6) listening and composing replies to e-mail/text messages read by a “synthetic” voice, 7) interacting with a menu-based system with perfect reliability, 8), interacting with a menu-based system with moderate reliability, and 9) using “hands-free” Siri to listen to and send text messages, update Facebook or Twitter status, and modify and review calendar appointments. Because each task allowed the driver to keep his or her eyes on the road and hands on the steering wheel, any impairment to driving must be caused by the diversion of attention from the task of operating the motor vehicle. The authors used a combination of primary-task, secondary-task, subjective, and psychophysiological indices to assess the mental workload of the driver using these voice-based technologies. The data extend the rating system for cognitive distraction developed by Strayer et al., (2013). The new ratings suggest that some voice-based interactions in the vehicle may have unintended consequences that adversely affect traffic safety.
Ischemia-reperfusion injury. (1993)

Ischemia followed by reperfusion of the rat hind limb resulted in local evidence of injury, as reflected in increased vascular permeability and hemorrhage in skeletal muscle as well as distant organ injury, as reflected by increased vascular permeability and hemorrhage in lung. These changes were proportional to the duration of reperfusion and were associated with neutrophil accumulation in tissue, as quantitated by myeloperoxidase (MPO) content. There was corresponding evidence of complement depletion and increases in plasma IL-1 and IL-6. On the basis of interventional approaches, limb and lung vascular injury was neutrophil and complement dependent and was attenuated by treatment with antioxidants. Products of L-arginine were involved in the development of vascular injury since antagonists of L-arginine were protective. Based on the use of blocking antibodies, the cytokines TNF alpha and IL-1 were also involved in the development of tissue injury. Finally, both LFA-1 (CD11a/CD18) and Mac-1 (CD11b/CD18) beta 2 integrins were required as well as the endothelial adhesion molecules E-selectin and ICAM-1. Protective interventions were more protective that both local and remote organ injury following ischemia-reperfusion is in lung than in skeletal muscle. There were, in general, parallel effects when tissue protection was related to reduction in MPO content. These data suggest dependent on toxic oxygen and L-arginine products of neutrophils, the accumulation of which can be linked to cytokines (TNF alpha, IL-1), beta 2 integrins and endothelial adhesion molecules.
Protein Kinase C (PKC)η-mediated PKCμ Activation Modulates ERK and JNK Signal Pathways (2002)

Protein kinase C (PKC), a family of lipid-activated serine kinases, is involved in multiple functions in the regulation of growth control. The PKC-related isoform PKC mu/PKD has been implicated in mitogenic signal cascades because of the activation of p42/p44 MAPK leading to Elk1-mediated gene transcription, and PKC mu/PKD has been shown to be activated via a PKC-dependent pathway. By using confocal analyses, we demonstrate here that PKC mu partially colocalizes with PKC eta in different cell types. Colocalization depends on the presence of the PKC mu pleckstrin homology domain. Coexpression of constitutively active PKC eta with PKC mu leads to a significant enhancement of the PKC mu substrate phosphorylation capacity as a result of an increased phosphorylation of the activation loop Ser(738/742) of PKC mu, whereas Ser(910) autophosphorylation remains unaffected. In vitro phosphorylation experiments show that PKC eta directly phosphorylates PKC mu on activation loop serines. Consequently, the p42 MAPK cascade is triggered leading to an increase in reporter gene activity driven by a serum-responsive element in HEK293 cells. At the same time, PKC eta-mediated JNK activation is reduced, providing evidence for a mutual regulation of PKC mu/PKC eta affecting different arms of the p38/ERK/JNK pathways. Our data provide evidence for the sequential involvement of selective PKC isoforms in kinase cascades and identify the relevant domains in PKC mu for interaction with and activation by PKC eta as pleckstrin homology domain and activation loop.
Saccharomyces boulardii Protease Inhibits the Effects of Clostridium difficile Toxins A and B in Human Colonic Mucosa (1999)

Saccharomyces boulardii is a nonpathogenic yeast used in the treatment of Clostridium difficile diarrhea and colitis. We have reported that S. boulardii inhibits C. difficile toxin A enteritis in rats by releasing a 54-kDa protease which digests the toxin A molecule and its brush border membrane (BBM) receptor (I. Castagliuolo, J. T. LaMont, S. T. Nikulasson, and C. Pothoulakis, Infect. Immun. 64:5225-5232, 1996). The aim of this study was to further evaluate the role of S. boulardii protease in preventing C. difficile toxin A enteritis in rat ileum and determine whether it protects human colonic mucosa from C. difficile toxins. A polyclonal rabbit antiserum raised against purified S. boulardii serine protease inhibited by 73% the proteolytic activity present in S. boulardii conditioned medium in vitro. The anti-protease immunoglobulin G (IgG) prevented the action of S. boulardii on toxin A-induced intestinal secretion and mucosal permeability to [3H]mannitol in rat ileal loops, while control rabbit IgG had no effect. The anti-protease IgG also prevented the effects of S. boulardii protease on digestion of toxins A and B and on binding of [3H]toxin A and [3H]toxin B to purified human colonic BBM. Purified S. boulardii protease reversed toxin A- and toxin B-induced inhibition of protein synthesis in human colonic (HT-29) cells. Furthermore, toxin A- and B-induced drops in transepithelial resistance in human colonic mucosa mounted in Ussing chambers were reversed by 60 and 68%, respectively, by preexposing the toxins to S. boulardii protease. We conclude that the protective effects of S. boulardii on C. difficile-induced inflammatory diarrhea in humans are due, at least in part, to proteolytic digestion of toxin A and B molecules by a secreted protease.
Air-Induced anti-Markovnikov Addition of Secondary Phosphine Oxides and H-Phosphinates to Alkenes (2006)

[reaction: see text] Air (oxygen) induces the addition of secondary phosphine oxides and H-phosphinates to alkenes to selectively produce the corresponding anti-Markovnikov adducts in good to high yields. Mechanistic studies show that the addition probably proceeds via a radical chain mechanism.
A passive micromachined device for alignment of arrays of single-mode fibers for manufacturable photonic packaging (2002)

Summary form only given. This work provides a method of passive mechanical alignment of an array of single mode fibers to an array of binary optics. The technique employs the use of a micro-machined metal spring, that captures a vertical, pre-positioned fiber, moves it into accurate alignment, and holds it for attachment.
Transplatin-Modified Oligo(2‘-O-methyl ribonucleotide)s:  A New Tool for Selective Modulation of Gene Expression (1997)

In the reaction between trans-diamminedichloroplatinum(II) and single-stranded oligo(2'-O-methyl ribonucleotide)s containing the sequence GNG (N being a nucleotide residue), the 1,3-trans-{Pt-(NH3)2[GNG]} cross-links are formed. The 1,3-intrastrand cross-links are inert within the single-stranded oligonucleotides. By contrast, they rearrange into interstrand cross-links when the platinated oligonucleotides are paired with their complementary RNA strands. The rate of the interstrand cross-linking reaction depends upon the sequence facing the intrastrand cross-links. When the complementary sequences are 5'-CN'C (N' being a nucleotide), the rates are rather slow (T1/2 >/= 3 h at 37 degrees C). The rearrangement of the intrastrand cross-links into interstrand cross-links can be achieved in a few minutes when the triplets facing the intrastrand cross-links are replaced by doublet 5'-UA or 5'-CA. In vitro, the specificity of the cross-linking reaction between a platinated oligo(2'-O-methyl ribonucleotide) and its target sequence (containing the 5'-CA doublet) located within the coding region of Ha-ras mRNA is demonstrated by steric blocking of reverse transcriptase and translation machinery. Within the HBL100ras1 cells, this platinated oligonucleotide binds specifically and irreversibly to the cognate Ha-ras mRNA. It also inhibits the proliferation of the HBL100ras1 cells in a dose-dependent manner. The fast and specific interstrand cross-linking reaction triggered by the formation of a double helix between platinated oligo(2'-O-methyl ribonucleotide)s and RNA enhances the potential of the oligonucleotides which do not induce mRNA cleavage by RNase H, to modulate gene expression by steric blocking of the translation machinery.
Combined audio and visual streams analysis for video sequence segmentation (2002)

We present a new approach to video sequence segmentation into individual shots. Unlike previous approaches, our technique segments the video sequence by combining two streams of information extracted from the visual track with audio track segmentation information. The visual streams of information are computed from the coarse data in a 3-D wavelet decomposition of the video track. They consist of (i) information derived from temporal edges detected along the time evolution of the intensity of each pixel in temporally sub-sampled spatially filtered coarse frames, and (ii) information derived from the coarse spatio-temporal evolution of intra-frame edges in the spatially filtered coarse frames. Our approach is particularly matched to progressively transmitted video.
Efficacy of Methotrexate in Rheumatoid Arthritis (1995)

Methotrexate (MTX), an antifolate agent, has been used in the treatment of rheumatoid arthritis (RA) for over two decades. Open clinical studies and short-term, randomized, placebo-controlled studies demonstrate the efficacy of MTX in active RA. Long-term prospective studies, including two of over 7 yr duration, report a sustained response and a corticosteroid-sparing effect. Comparative studies demonstrate superior efficacy to auranofin, azathioprine and cyclosporin A. A highly favourable retention rate with the drug has been noted in large studies from academic and community-based practices. Radiographic studies suggest a slowing of radiographic progression with the compound. MTX has become an accepted and widely used treatment for active RA.