gebhart/patrepeval huggingface dataset:
Tim-3 signaling in peripheral NK cells promotes maternal-fetal immune tolerance and alleviates pregnancy loss (2017)

Pregnancy loss occurs in about 15% of clinically recognized pregnancies, and defective maternal-fetal immune tolerance contributes to more than 50% of these events. We found that signaling by the type I membrane protein T cell immunoglobulin and mucin-containing protein 3 (Tim-3) in natural killer (NK) cells had an essential protective role during early pregnancy. Tim-3 on peripheral NK (pNK) cells was transiently increased in abundance during the first trimester of pregnancy, which depended on interleukin-4 (IL-4)-signal transducer and activator of transcription 6 (STAT6) and progesterone signaling. Tim-3<sup>+</sup> pNK cells displayed immunosuppressive activities, including the production of anti-inflammatory cytokines and the induction of regulatory T cells (T<sub>regs</sub>) in a transforming growth factor-β1 (TGF-β1)-dependent manner. Tim-3 on pNK cells was stimulated by its ligand galectin-9 (Gal-9), leading to signaling by the kinases c-Jun N-terminal kinase (JNK) and AKT. In recurrent miscarriage (RM) patients, Tim-3 abundance on pNK cells was reduced and the immunosuppressive activity of Tim-3<sup>+</sup> pNK cells was impaired. Compared to Tim-3<sup>+</sup> pNK cells from donors with normal pregnancies, RM patient Tim-3<sup>+</sup> pNK cells exhibited changes in DNA accessibility in certain genetic loci, which were reversed by inhibiting accessible chromatin reader proteins. Furthermore, Tim-3<sup>+</sup> pNK cells, but not Tim-3<sup>-</sup> pNK cells, reduced fetal loss in abortion-prone and NK cell-deficient mice. Together, our findings reveal a critical role for Tim-3-Gal-9 signaling-mediated immunoregulation by pNK cells in maternal-fetal immune tolerance and suggest that Tim-3 abundance on pNK cells is a potential biomarker for RM diagnosis.
Cloning and characterization of the human homologue of a dystrophin related phosphoprotein found at the Torpedo electric organ post- synaptic membrane (1996)

Dystrophin is the protein product which is absent in Duchenne muscular dystrophy (DMD). In mammalian skeletal muscle, dystrophin is found in association with several integral and peripheral membrane proteins, forming a complex known as the dystrophin glycoprotein complex (DGC). In an expressed sequence tag (EST) database search to identify new dystrophin related genes, we isolated EST00891 which showed 57% homology to the cysteine-rich domain of dystrophin and localized to 18q12.1-12.2. This EST is also highly homologous (90%) to the Torpedo californica post-synaptic 87 kDa phosphoprotein. Screening human adult brain and skeletal muscle cDNA libraries with this EST resulted in cloning multiple cDNAs which encode several splice forms all homologous to the C-terminal domain of dystrophin. The largest open reading frame isolated shows 94% homology (86% identity) to the Torpedo 87 kDa protein and 50% homology to the cysteine-rich and carboxy-terminal domains of dystrophin. The other cDNAs isolated encode smaller splice forms of this gene which we have named dystrobrevin. The tissue distribution of dystrobrevin mRNA shows five distinct transcripts which are preferentially expressed between different tissues. In addition, antibodies against either the Torpedo 87 kDa protein or human dystrobrevin demonstrate that at least three of the splice forms are translated as proteins in human brain tissue extracts.
Diagnostic criteria for hematopoietic stem cell transplant-associated microangiopathy: results of a consensus process by an International Working Group (2007)

The Working Group recommends that the presented criteria of TAM be adopted in clinical use, especially in scientific trials.
Tm(DOTP)5−: A 23Na+ shift agent for perfused rat hearts (1990)

Tm(DOTP)5-, the thulium(III) complex of 1,4,7,10-tetraazacyclododecane-N,N',N',N'''-tetra(methylenephos p hon ate), is introduced as a 23Na+ shift agent for use in discrimination of the NMR resonances of intra- and extracellular 23Na+ ions in perfused rat hearts. The novel shift agent is directly compared to the widely used Dy(TTHA)3- (dysprosium(III) triethylenetetraminehexaacetate).
The origin of follicular dendritic cells in the mouse and the mechanism of trapping of immune complexes on them (1984)

F1----parental bone marrow chimeras between CBA and B10 mice were used to show that even after 1 year follicular dendritic cells (FDC), also termed dendritic reticular cells, are not derived from bone marrow stem cells. However clusters of cells wrapped in the dendritic processes of FDC, isolated by enzyme digestion of the spleen contain B cells originating from donor marrow. This implies that evidence for the presence of antigens such as Ia-like detected by others (Gerdes, J. and Stein, H., Clin. Exp. Immunol. 1982. 48: 348) by immunohistology in or on FDC clusters should be interpreted with caution. Deposition of immune complexes on mouse spleen FDC depends upon the presence of a radio- and cyclophosphamide-sensitive population of cells, although FDC themselves are resistant to such treatments. After whole body irradiation the capacity to localize fluorescein isothiocyanate-labeled aggregated human gamma globulin can be restored by normal or T-deprived spleen cells, but restoration requires an interval of more than 1 though less than 5 days. These findings are compatible with the evidence of Gray et al., Eur. J. Immunol. 1984. 14: 47, that in the rat immune complexes are transported to FDC by a sessile population of marginal zone lymphocytes, as first suggested by Brown et al., Immunology 1973. 24: 955.
The $1,000 Genome: The Revolution in DNA Sequencing and the New Era of Personalized Medicine (2010)

In 2000, President Bill Clinton signaled the completion of the Human Genome Project at a cost in excess of $2 billion. A decade later, the price for any of us to order our own personal genome sequence--a comprehensive map of the 3 billion letters in our DNA--is rapidly and inevitably dropping to just $1,000. Dozens of men and women--scientists, entrepreneurs, celebrities, and patients--have already been sequenced, pioneers in a bold new era of personalized genomic medicine. $1,000 genome has long been considered the tipping point that would open the floodgates to this revolution. Do you have gene variants associated with Alzheimer's or diabetes, heart disease or cancer? Which drugs should you consider taking for various diseases, and at what dosage? In the years to come, doctors will likely be able to tackle all of these questions--and many more--by using a computer in their offices to call up your unique genome sequence, which will become as much a part of your medical record as your blood pressure. Indeed, many experts are advocating that all newborns have a complete genome analysis done so that preventive measures and preemptive medicine can begin early in life. How has this astonishing achievement been accomplished? And what will it mean for our lives? To research the story of this unfolding revolution, critically acclaimed science writer Kevin Davies has spent the past few years traveling to the leading centers and interviewing the entrepreneurs and pioneers in the race to achieve the $1,000 genome. He vividly brings to life the extraordinary drama of this grand scientific achievement, revealing the masterful ingenuity that has transformed the process of decoding DNA and delivering the information it possesses to the public at large. Davies also profiles the future of genomic medicine and thoughtfully explores the many pressing issues raised by the tidal wave of personal genetic information. Will your privacy be protected? Will you be pressured, by insurance companies or by your employer, to get your genome sequenced? What psychological toll might there be to discovering you are at risk for certain diseases like Alzheimer's? And will the government or the medical establishment come between you and your genome? One thing that not in question that we are moving swiftly into the personalized medicine era, and The $1,000 Genome is an essential guide to this brave new future.
Linearization and Scatter-Correction for Near-Infrared Reflectance Spectra of Meat (1985)

This paper is concerned with the quantitative analysis of multicomponent mixtures by diffuse reflectance spectroscopy. Near-infrared reflectance (NIRR) measurements are related to chemical composition but in a nonlinear way, and light scatter distorts the data. Various response linearizations of reflectance (R) are compared ( R with Saunderson correction for internal reflectance, log 1/ R, and Kubelka-Munk transformations and its inverse). A multi-wavelength concept for optical correction (Multiplicative Scatter Correction, MSC) is proposed for separating the chemical light absorption from the physical light scatter. Partial Least Squares (PLS) regression is used as the multivariate linear calibration method for predicting fat in meat from linearized and scatter-corrected NIRR data over a broad concentration range. All the response linearization methods improved fat prediction when used with the MSC; corrected log 1/ R and inverse Kubelka-Munk transformations yielded the best results. The MSC provided simpler calibration models with good correspondence to the expected physical model of meat. The scatter coefficients obtained from the MSC correlated with fat content, indicating that fat affects the NIRR of meat with an additive absorption component and a multiplicative scatter component.
Expression and Cellular Immunogenicity of a Transgenic Antigen Driven by Endogenous Poxviral Early Promoters at Their Authentic Loci in MVA (2012)

CD8(+) T cell responses to vaccinia virus are directed almost exclusively against early gene products. The attenuated strain modified vaccinia virus Ankara (MVA) is under evaluation in clinical trials of new vaccines designed to elicit cellular immune responses against pathogens including Plasmodium spp., M. tuberculosis and HIV-1. All of these recombinant MVAs (rMVA) utilize the well-established method of linking the gene of interest to a cloned poxviral promoter prior to insertion into the viral genome at a suitable locus by homologous recombination in infected cells. Using BAC recombineering, we show that potent early promoters that drive expression of non-functional or non-essential MVA open reading frames (ORFs) can be harnessed for immunogenic expression of recombinant antigen. Precise replacement of the MVA orthologs of C11R, F11L, A44L and B8R with a model antigen positioned to use the same translation initiation codon allowed early transgene expression similar to or slightly greater than that achieved by the commonly-used p7.5 or short synthetic promoters. The frequency of antigen-specific CD8(+) T cells induced in mice by single shot or adenovirus-prime, rMVA-boost vaccination were similarly equal or marginally enhanced using endogenous promoters at their authentic genomic loci compared to the traditional constructs. The enhancement in immunogenicity observed using the C11R or F11L promoters compared with p7.5 was similar to that obtained with the mH5 promoter compared with p7.5. Furthermore, the growth rates of the viruses were unimpaired and the insertions were genetically stable. Insertion of a transgenic ORF in place of a viral ORF by BAC recombineering can thus provide not only a potent promoter, but also, concomitantly, a suitable insertion site, potentially facilitating development of MVA vaccines expressing multiple recombinant antigens.
Glucocorticoid regulation of metallothionein-I mRNA synthesis in cultured mouse cells. (1981)

Eight mouse cell lines were tested for their ability to accumulate metallothionein-I mRNA in response to dexamethasone or cadmium; 5 respond to both inducers, 1 responds to cadmium only, and 2 lymphoid lines respond to neither inducer. The glucocorticoid response was analyzed further using the sarcoma cell line (S180). Metallothionein-I mRNA synthesis increases 5-fold within 1 h of dexamethasone addition and closely parallels the accumulation of nuclear glucocorticoid receptors. Both metallothionein-I mRNA levels and metallothionein synthesis increase coordinately in response to dexamethasone and reach a new steady state by 8 h that is 10-fold higher than control values. Induction of metallothionein-I mRNA appears to be independent of dexamethasone effects on zinc uptake and does not require concomitant protein synthesis.
Genomic Loss of microRNA-101 Leads to Overexpression of Histone Methyltransferase EZH2 in Cancer (2008)

Enhancer of zeste homolog 2 (EZH2) is a mammalian histone methyltransferase that contributes to the epigenetic silencing of target genes and regulates the survival and metastasis of cancer cells. EZH2 is overexpressed in aggressive solid tumors by mechanisms that remain unclear. Here we show that the expression and function of EZH2 in cancer cell lines are inhibited by microRNA-101 (miR-101). Analysis of human prostate tumors revealed that miR-101 expression decreases during cancer progression, paralleling an increase in EZH2 expression. One or both of the two genomic loci encoding miR-101 were somatically lost in 37.5% of clinically localized prostate cancer cells (6 of 16) and 66.7% of metastatic disease cells (22 of 33). We propose that the genomic loss of miR-101 in cancer leads to overexpression of EZH2 and concomitant dysregulation of epigenetic pathways, resulting in cancer progression.
Threshold logic (1971)

A threshold gate has binary inputs and outputs just like any other logic gate. The difference, however, is that in the threshold gate the inputs may be weighted and, eventually, a binary decision made as to whether the total weight is more or less than some reference. This principle of weighting and summing the inputs rather than simply noting the presence of all inputs as high (as in an AND gate) or one input high (as in an OR gate) is the reason that a threshold gate can tell more about the state of the inputs, thus providing greater ``logic power.'' This article gives some examples of the applicability of threshold logic, as well as an integrated-circuit approach for building arrays of versatile threshold gates. In addition, some logic designs are described and compared with conventional ECL implementations.
Endocrine and Intracrine Sources of Androgens in Women: Inhibition of Breast Cancer and Other Roles of Androgens and Their Precursor Dehydroepiandrosterone (2003)

Serum androgens as well as their precursors and metabolites decrease from the age of 30-40 yr in women, thus suggesting that a more physiological hormone replacement therapy at menopause should contain an androgenic compound. It is important to consider, however, that most of the androgens in women, especially after menopause, are synthesized in peripheral intracrine tissues from the inactive precursors dehydroepiandrosterone (DHEA) and DHEA sulfate (DHEA-S) of adrenal origin. Much progress in this new area of endocrine physiology called intracrinology has followed the cloning and characterization of most of the enzymes responsible for the transformation of DHEA and DHEA-S into androgens and estrogens in peripheral target tissues, where the locally produced sex steroids are exerting their action in the same cells in which their synthesis takes place without significant diffusion into the circulation, thus seriously limiting the interpretation of serum levels of active sex steroids. The sex steroids made in peripheral tissues are then inactivated locally into more water-soluble compounds that diffuse into the general circulation where they can be measured. In a series of animal models, androgens and DHEA have been found to inhibit breast cancer development and growth and to stimulate bone formation. In clinical studies, DHEA has been found to increase bone mineral density and to stimulate vaginal maturation without affecting the endometrium, while improving well-being and libido with no significant side effects. The advantage of DHEA over other androgenic compounds is that DHEA, at physiological doses, is converted into androgens and/or estrogens only in the specific intracrine target tissues that possess the appropriate physiological enzymatic machinery, thus limiting the action of the sex steroids to those tissues possessing the tissue-specific profile of expression of the genes responsible for their formation, while leaving the other tissues unaffected and thus minimizing the potential side effects observed with androgens or estrogens administered systemically.
In vivo multicolor molecular MR imaging using diamagnetic chemical exchange saturation transfer liposomes (2011)

A variety of (super)paramagnetic contrast agents are available for enhanced MR visualization of specific tissues, cells, or molecules. To develop alternative contrast agents without the presence of metal ions, liposomes were developed containing simple bioorganic and biodegradable compounds that produce diamagnetic chemical exchange saturation transfer MR contrast. This diamagnetic chemical exchange saturation transfer contrast is frequency-dependent, allowing the unique generation of "multicolor" images. The contrast can be turned on and off at will, and standard images do not show the presence of these agents. As an example, glycogen, L-arginine, and poly-L-lysine were encapsulated inside liposomes and injected intradermally into mice to image the lymphatic uptake of these liposomes. Using a frequency-dependent acquisition scheme, it is demonstrated that multicolor MRI can differentiate between different contrast particles in vivo following their homing to draining lymph nodes. Being nonmetallic and bioorganic, these diamagnetic chemical exchange saturation transfer liposomes form an attractive novel platform for multicolor imaging in vivo.
Grifola frondosa water extract alleviates intestinal inflammation by suppressing TNF-α production and its signaling (2010)

TNF-alpha is a major cytokine involved in inflammatory bowel disease (IBD). In this study, water extract of Grifola frondosa (GFW) was evaluated for its protective effects against colon inflammation through the modulation of TNF-alpha action. In coculture of HT-29 human colon cancer cells with U937 human monocytic cells, TNF-alpha-induced monocyte adhesion to HT-29 cells was significantly suppressed by GFW (10, 50, 100 micg/ml). The reduced adhesion by GFW correlated with the suppressed expression of MCP-1 and IL-8, the major IBD-associated chemokines. In addition, treatment with GFW significantly suppressed TNF-alpha-induced reactive oxygen species production and NF-kappaB transcriptional activity in HT-29 cells. In differentiated U937 monocytic cells, LPS-induced TNF-alpha production, which is known to be mediated through NF-kappaB activation, was significantly suppressed by GFW. In an in vivo rat model of IBD, oral administration of GFW for 5 days (1 g/kg per day) significantly inhibited the trinitrobenzene sulfonic acid (TNBS)-induced weight loss, colon ulceration, myeloperoxidase activity, and TNF-alpha expression in the colon tissue. Moreover, the effect of GFW was similar to that of intra-peritoneal injection of 5-aminosalicylic acid (5-ASA), an active metabolite of sulfasalazine, commonly used drug for the treatment of IBD. The results suggest that GFW ameliorates colon inflammation by suppressing production of TNF-alpha as well as its signaling through NF-kappaB leading to the expression of inflammatory chemokines, MCP-1 and IL-8. Taken together, the results strongly suggest GFW is a valuable medicinal food for IBD treatment, and thus may be used as an alternative medicine for IBD.
The histone methyltransferase, NSD2, enhances androgen receptor‐mediated transcription (2009)

In this study, we discovered that NSD2 specifically interacts with the DNA-binding domain of androgen receptor (AR) via its HMG domain, and the nuclear translocation of both NSD2 and AR is enhanced in the presence of ligand. Furthermore, we also demonstrated that the over expression of NSD2, but not of NSD2 (DeltaSET) HMT-activity defective mutant, enhanced the mRNA level of PSA in a dose-dependent manner. A chromatin immunoprecipitation assay showed that NSD2 protein is recruited to the enhancer region of the PSA gene by AR in an agonist-enhanced manner. Taken together, these results uncover a potential role for NSD2 in AR-mediated transcription, implicating NSD2 in prostate carcinogenesis.
Nuclear Gene Genealogies Reveal Historical, Demographic and Selective Factors Associated With Speciation in Field Crickets (2003)

Population genetics theory predicts that genetic drift should eliminate shared polymorphism, leading to monophyly or exclusivity of populations, when the elapsed time between lineage-splitting events is large relative to effective population size. We examined patterns of nucleotide variation in introns at four nuclear loci to relate processes affecting the history of genes to patterns of divergence among natural populations and species. Ancestral polymorphisms were shared among three recognized species, Gryllus firmus, G. pennsylvanicus, and G. ovisopis, and genealogical patterns suggest that successive speciation events occurred recently and rapidly relative to effective population size. High levels of shared polymorphism among these morphologically, behaviorally, and ecologically distinct species indicate that only a small fraction of the genome needs to become differentiated for speciation to occur. Among the four nuclear gene loci there was a 10-fold range in nucleotide diversity, and patterns of polymorphism and divergence suggest that natural selection has acted to maintain or eliminate variation at some loci. While nuclear gene genealogies may have limited applications in phylogeography or other approaches dependent on population monophyly, they provide important insights into the historical, demographic, and selective forces that shape speciation.
Fire at Notre Dame Cathedral and Lead Materials in the Environment (2020)

This literature review deals with lead materials in fire and related environmental issues based on inorganic chemistry.In 2019, the Notre Dame Cathedral fire raised not only the issue of damage to historical building, but also the issue of the impact of lead materials on the environment as well as human health.Three months after the fire, French media reported that lead contamination had been detected in the area around the cathedral, with lead levels 500-800 times higher than the safety requirements.More than 200 tons of lead used in the roofs and spire melted in the fire.Besides this French fire case, chemical aspects of lead (element and compounds), usage of lead as building materials (Japanese castle, paint for a highway bridge, and protection against radioactive rays) on past architectural fires, energy materials (gasoline, lead-acid battery, and Perovskites solar cells in future) and their potential fire risk, and impact to human are also reviewed in this paper.
Catalytic Three‐Component Coupling of Alkynes, Imines, and Organoboron Reagents. (2003)

Abstract For Abstract see ChemInform Abstract in Full Text.