gebhart/patrepeval huggingface dataset:
The Handbook of infrared and Raman characteristic frequencies of organic molecules (1992)

Alkanes. Halocompounds. Alcohols and Phenols. Ethers and Peroxides. Alkenes. Acetylenes. The -C=N and -N=C Groups. Compounds Containing the Carbonyl Group. Compounds Containing -NH2, -NHR, and -NR2 Groups. The Nitro Group. Double Bonds Containing Nitrogen Atoms. Cumulated Double Bonds. Organic Sulfur Compounds. Organosilicon Compounds. Organophosphorous Compounds. Aromatic and Heteroaromatic Rings. Selected Infrared and Raman Spectra. Appendices. Index.
VASCULAR RISK FACTORS AND DEMENTIA: HOW TO MOVE FORWARD? (2009)

Viswanathan et al.1 present a thoughtful, timely, and alternative approach to the classification of dementia. Specifically, they stress the importance of vascular factors on Alzheimer disease (AD) and of viewing dementia as a continuum of purely neurodegenerative dementia, purely vascular dementia, and as the combination of both vascular and degenerative contributions seen in some cases. The consideration of other etiologies is also important in the evaluation of dementia. Other diseases may clinically present like AD, including hereditary diffuse leukoencephalopathy with spheroids (HDLS).

HDLS is an autosomal dominant …
New .alpha.-methylene .gamma.-lactone derivatives of substituted nucleic acid bases as potential anticancer agents (1986)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTNew .alpha.-methylene .gamma.-lactone derivatives of substituted nucleic acid bases as potential anticancer agentsUtpal Sanyal, Saktimoyee Mitra, Prasun Pal, and S. K. ChakrabortiCite this: J. Med. Chem. 1986, 29, 5, 595–599Publication Date (Print):May 1, 1986Publication History Published online1 May 2002Published inissue 1 May 1986https://pubs.acs.org/doi/10.1021/jm00155a001https://doi.org/10.1021/jm00155a001research-articleACS PublicationsRequest reuse permissionsArticle Views209Altmetric-Citations21LEARN 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
Cloning and sequencing of a human thioredoxin reductase (1995)

The DNA sequence encoding human placental thioredoxin reductase has been determined. Of the 3826 base pairs sequenced, 1650 base pairs were in an open reading frame encoding a mature protein with 495 amino acids and a calculated molecular mass of 54,171. Sequence analysis showed strong similarity to glutathione reductases and other NADPH-dependent reductases. Human thioredoxin reductase contains the redox-active cysteines in the putative FAD binding domain and has a dimer interface domain not previously seen with prokaryote and lower eukaryote thioredoxin reductases.
The atomic structure of adeno-associated virus (AAV-2), a vector for human gene therapy (2002)

The structure of the adeno-associated virus (AAV-2) has been determined to 3-A resolution by x-ray crystallography. AAV is being developed as a vector for gene therapy to treat diseases including hemophilia, cancer, and cystic fibrosis. As in the distantly related autonomous parvoviruses, the capsid protein has a beta-barrel fold, but long loops between the beta-strands share little structural homology with other parvoviruses, leading to unique surface features. Most prominent are groups of threefold-related peaks, each an intimate association of loops from two neighboring subunits. Mutations affecting cell entry and receptor binding are clustered near the positively charged side of each peak, implicating the region in attachment to the cellular receptor, heparan sulfate proteoglycan. Amino acids involved in antibody binding are in the same general vicinity. The structure will guide rational engineering of vector capsids to tailor cellular targeting and to avoid immediate neutralization by an immune system sensitized by prior exposure to AAV.
Phosphorylation of Eukaryotic Translation Initiation Factor 2 Mediates Apoptosis in Response to Activation of the Double-stranded RNA-dependent Protein Kinase (1998)

The interferon-inducible, double-stranded (ds) RNA-dependent serine/threonine protein kinase (PKR) plays a role in viral pathogenesis, cell growth, and differentiation and is implicated as a tumor suppressor gene. Expression of a trans-dominant negative, catalytically inactive mutant PKR protected NIH3T3 cells from apoptosis in response to either treatment with tumor necrosis factor alpha (TNF alpha), serum deprivation. In cells expressing mutant PKR, TNF alpha, but not dsRNA induced transcription from a nuclear factor kappa B-dependent promoter, demonstrating specificity for dsRNA in signaling through the PKR pathway. Serum or platelet-derived growth factor addition to serum-deprived mutant PKR-expressing cells induced transcription of the early response genes c-fos and c-jun, indicating that the immediate early response signaling was intact. Overexpression of wild-type PKR in a transient DNA transfection system was sufficient to induce apoptosis. TNF alpha-induced apoptosis correlated with increased phosphorylation of the alpha subunit of eukaryotic translation initiation factor 2 (eIF-2 alpha), the primary physiological substrate of the PKR. Furthermore, forced expression of a nonphosphorylatable S51A mutant eIF-2 alpha partially protected cells from TNF alpha-induced apoptosis, and expression of a S51D mutant eIF-2 alpha, a mutant that mimics phosphorylated eIF-2 alpha, was sufficient to induce apoptosis. Taken together, these studies identify a novel requirement for PKR in stress-induced apoptosis that is mediated through eIF-2 alpha phosphorylation.
Three hydrates of the bisphosphonate risedronate, consisting of one molecular and two ionic structures (2003)

Three different hydrates of risedronate were obtained by varying the pH of a solution containing the compound. At the pH values used, the N atom of the pyridine group is protonated and the compounds are zwitterionic. Crystals obtained directly from the synthesis resulted in risedronate monohydrate, or [1-hydroxy-1-phosphono-2-(pyridinium-3-yl)ethyl]phosphonate monohydrate, C(7)H(11)NO(7)P(2).H(2)O, (I), in which just one phosphonate group is negatively charged. Recrystallizations at pH values of 2 and 4 yielded risedronate dihydrate, or sodium [1-hydroxy-2-(pyridinium-3-yl)ethane-1,2-diyl]bis(phosphonate) dihydrate, Na(+).C(7)H(10)NO(7)P(2)(-).2H(2)O, (II). Finally, recrystallizations at pH values of 7 and 8 produced risedronate 2.5-hydrate, or sodium [1-hydroxy-2-(pyridinium-3-yl)ethane-1,2-diyl]bis(phosphonate) 2.5-hydrate, Na(+).C(7)H(10)NO(7)P(2)(-).2.5H(2)O, (III). At these four pH values, both phosphonate groups in (II) and (III) are negatively charged and coordinated to an Na(+) ion. Crystals of (II), i.e. those grown at pH values of 2 and 4, have isomorphous polymeric ion aggregate structures with geminal phosphonate and alcohol groups coordinated to the same Na(+) ion. On the other hand, crystals of (III), i.e. those grown at pH values of 7 and 8, have isomorphism polymeric ion aggregate structures with geminal phosphonate and alcohol groups coordinated to different Na(+) ions.
Glucagon‐like peptide‐1(7–36) amide is a new incretin/enterogastrone candidate (1991)

Peer Reviewed
Role of an RNA cleavage/poly(A) addition site in the production of membrane-bound and secreted IgM mRNA. (1985)

The switch from membrane-bound to secreted IgM is accomplished by producing alternative forms of mRNA from a single mu heavy-chain gene. This process might be controlled at any of three steps--transcription termination, RNA splicing, or RNA cleavage/poly(A) addition. To distinguish between these possibilities, we have constructed a model human mu gene and observed its expression in early- and late-stage murine B cells. In each case, expression of the model gene reflects the state of development of the host cell; i.e., more of the mRNA for membrane-bound IgM is made in early B cells and more of the secreted form is made in late B cells. Using systematic deletions and analyses of RNA products of the model gene, we implicate RNA cleavage/poly(A) addition as the governing reaction. Removal of the cleavage/poly(A) signal for secreted mu mRNA by a series of BAL-31 deletions produces not only a decrease in secreted mu mRNA but also a compensatory increase in the membrane-bound form. Further, transcripts that do not terminate to the 5' side of the membrane anchor exons are found in cells producing only secreted IgM. As defined by these deletions, we establish that the RNA cleavage signal spans at least 35 bases and speculate that it forms an RNA stemloop that may be important in 3' end formation.
Yeast-like chronological senescence in mammalian cells: phenomenon, mechanism and pharmacological suppression (2011)

In yeast, chronological senescence (CS) is defined as loss of viability in stationary culture. Although its relevance to the organismal aging remained unclear, yeast CS was one of the most fruitful models in aging research. Here we described a mammalian replica of yeast CS: loss of viability of overgrown "yellow" cancer cell culture. In a density and time (chronological)-dependent manner, cell culture loses the ability to re-grow in fresh medium. Rapamycin dramatically decelerated CS. Loss of viability was caused by acidification of the medium by lactic acid (lactate). Rapamycin decreased production of lactate, making conditioned medium (CM) less deadly. Both deadly CM and lactate caused loss of viability in low cell density, not preventable by either rapamycin or additional glucose. Also, NAC, LY294002, U0126, GSK733, which all indirectly inhibit mTOR and have been shown to suppress the senescent phenotype in traditional models of mammalian cell senescence, also decreased lactate production and decelerated CS. We discuss that although CS does not mimic organismal aging, the same signal transduction pathways that drive CS also drive aging.
Growing bioengineered teeth from single cells: potential for dental regenerative medicine (2008)

The bioengineering techniques developed for tooth regeneration will in the future make substantial contributions to the ability to grow primordial organs in vitro and also to grow fully functioning organs, such as the liver, kidney and heart.
IL-12p35-Deficient Mice Are Susceptible to Experimental Autoimmune Encephalomyelitis: Evidence for Redundancy in the IL-12 System in the Induction of Central Nervous System Autoimmune Demyelination (2002)

Experimental autoimmune encephalomyelitis (EAE) serves as a model for multiple sclerosis and is considered a CD4(+), Th1 cell-mediated autoimmune disease. IL-12 is a heterodimeric cytokine, composed of a p40 and a p35 subunit, which is thought to play an important role in the development of Th1 cells and can exacerbate EAE. We induced EAE with myelin oligodendrocyte glycoprotein (MOG) peptide 35-55 (MOG(35-55)) in C57BL/6 mice and found that while IL-12p40-deficient (-/-) mice are resistant to EAE, IL-12p35(-/-) mice are susceptible. Typical spinal cord mononuclear cell infiltration and demyelination were observed in wild-type and IL-12p35(-/-) mice, whereas IL-12p40(-/-) mice had normal spinal cords. A Th1-type response to MOG(35-55) was observed in the draining lymph node and the spleen of wild-type mice. A weaker MOG(35-55)-specific Th1 response was observed in IL-12p35(-/-) mice, with lower production of IFN-gamma. By contrast, a Th2-type response to MOG(35-55) correlated with disease resistance in IL-12p40(-/-) mice. Production of TNF-alpha by microglia, CNS-infiltrating macrophages, and CD4(+) T cells was detected in wild-type and IL-12p35(-/-), but not in IL-12p40(-/-), mice. In addition, NO production was higher in IL-12p35(-/-) and wild-type mice than in IL-12p40(-/-) mice. These data demonstrate a redundancy of the IL-12 system in the induction of EAE and suggest that p40-related heterodimers, such as the recently cloned IL-23 (p40p19), may play an important role in disease pathogenesis.
Control and complications of intermittent heparin therapy. (1977)

A prospective study using an intermittent six hour method of heparin administration with control of subsequent dosage by the activated partial thromboplastin time revealed an over-all incidence of hemorrhagic complications of 12 per cent. If surgical patients are excluded, the incidence of hemorrhage falls to 4 per cent. This may be further reduced by monitoring the activated partial thromboplastin time within the therapeutic range. In no patient did thromboembolism recur while receiving heparin. It is suggested that this method provides adequate control of heparin therapy with an acceptable complication rate and adequate thromboembolic control and is cheaper to use than a continuous infusion.
A browser for bibliographic information retrieval, based on an application of lattice theory (1993)

An application of mathematical lattice theory, called relationship lattices, is utilized to attack problems of operational bibliographic information retrieval.The proposed solution offers an interface to the information searcher enabling operation in a world of concepts, authors, and document records and their relationships. This hides the complexities of query language and database structures, and it allows to use a personally preferred terminology and to browse, query and download document records in a convenient way.The main component of the proposed solution is a personal thesaurus built up as a relationship lattice.
Virulence of enterohemorrhagic Escherichia coli O91:H21 clinical isolates in an orally infected mouse model (1993)

Escherichia coli K-12 strains producing high levels of Shiga-like toxin type II (SLT-II) but not SLT-I were previously shown to be virulent in an orally infected, streptomycin-treated mouse model. In this investigation, we tested the virulence of several SLT-II-producing enterohemorrhagic E. coli (EHEC) isolates from patients with hemorrhagic colitis or hemolytic uremic syndrome. All of the strains tested were able to colonize the mouse intestine. However, only two strains were consistently virulent for mice: O91:H21 strain B2F1 (Strr), which was previously shown to carry two copies of slt-II-related toxins, and O91:H21 strain H414-36/89 (Strr), which was found in this study to contain three genes from the slt-II group. The oral 50% lethal doses of strains B2F1 (Strr) and H414-36/89 (Strr) when fed to streptomycin-treated mice were less than 10 bacteria. Histological sections from moribund mice fed the O91:H21 strains demonstrated extensive renal tubular necrosis; however, hematological results were not consistent with a diagnosis of hemolytic uremic syndrome. The central role of SLT in the virulence of the O91:H21 EHEC strains was supported by the finding that streptomycin-treated mice preinoculated with monoclonal antibody specific for SLT-II survived oral challenge with either B2F1 (Strr) or H414-36/89 (Strr). The basis for the variation in virulence among the SLT-II-producing EHEC strains tested was not determined. However, a correlation between the capacity of an EHEC strain to grow in small intestinal mucus and lethality in the streptomycin-treated mice was observed.
Dual Inhibition of Class IA Phosphatidylinositol 3-Kinase and Mammalian Target of Rapamycin as a New Therapeutic Option for T-Cell Acute Lymphoblastic Leukemia (2009)

Recent investigations have documented that constitutively activated phosphatidylinositol 3-kinase (PI3K)/Akt/mammalian target of rapamycin (mTOR) signaling is a common feature of T-cell acute lymphoblastic leukemia (T-ALL), where it strongly influences growth and survival. These findings lend compelling weight for the application of PI3K/Akt/mTOR inhibitors in T-ALL. However, our knowledge of PI3K/Akt/mTOR signaling in T-ALL is limited and it is not clear whether it could be an effective target for innovative therapeutic strategies. Here, we have analyzed the therapeutic potential of the dual PI3K/mTOR inhibitor PI-103, a small synthetic molecule of the pyridofuropyrimidine class, on both T-ALL cell lines and patient samples, which displayed constitutive activation of PI3K/Akt/mTOR signaling. PI-103 inhibited the growth of T-ALL cells, including 170-kDa P-glycoprotein overexpressing cells. PI-103 cytotoxicity was independent of p53 gene status. PI-103 was more potent than inhibitors that are selective only for PI3K (Wortmannin, LY294002) or for mTOR (rapamycin). PI-103 induced G(0)-G(1) phase cell cycle arrest and apoptosis, which was characterized by activation of caspase-3 and caspase-9. PI-103 caused Akt dephosphorylation, accompanied by dephosphorylation of the Akt downstream target, glycogen synthase kinase-3beta. Also, mTOR downstream targets were dephosphorylated in response to PI-103, including p70S6 kinase, ribosomal S6 protein, and 4E-BP1. PI-103 strongly synergized with vincristine. These findings indicate that multitargeted therapy toward PI3K and mTOR alone or with existing drugs may serve as an efficient treatment toward T-ALL cells, which require up-regulation of PI3K/Akt/mTOR signaling for their survival and growth.
Antibody-probed conformational transitions in the protease domain of human factor IX upon calcium binding and zymogen activation: putative high-affinity Ca(2+)-binding site in the protease domain. (1992)

The Fab fragment of a monoclonal antibody (mAb) reactive to the N-terminal half (residues 180-310) of the protease domain of human factor IX has been previously shown to inhibit the binding of factor IXa to its cofactor, factor VIIIa. These data suggested that this segment of factor IXa may participate in binding to factor VIIIa. We now report that the binding rate (kon) of the mAb is 3-fold higher in the presence of Ca2+ than in its absence for both factors IX and IXa; the half-maximal effect was observed at approximately 300 microM Ca2+. Furthermore, the off rate (koff) of the mAb is 10-fold higher for factor IXa than for factor IX with or without Ca2+. Moreover, like the kon for mAb binding, the incorporation of dansyl-Glu-Gly-Arg chloromethyl ketone (dEGR-CK) into factor IXa was approximately 3 times faster in the presence of Ca2+ than in its absence. Since steric factors govern the kon and the strength of noncovalent interactions governs the koff, the data indicate that the region of factor IX at residues 180-310 undergoes two separate conformational changes before expression of its biologic activity: one upon Ca2+ binding and the other upon zymogen activation. Furthermore, the dEGF-CK incorporation data suggest that both conformational changes also affect the active site residues. Analyses of the known three-dimensional structures of serine proteases indicate that in human factor IX a high-affinity Ca(2+)-binding site may be formed by the carboxyl groups of glutamates 235 and 245 and by the main chain carbonyl oxygens of residues 237 and 240. In support of this conclusion, a synthetic peptide including residues 231-265 was shown to bind Ca2+ with a Kd of approximately 500 microM. This peptide also bound to the mAb, although with approximately 500-fold reduced affinity. Moreover, like factor IX, the peptide bound to the mAb more strongly (approximately 3-fold) in the presence of Ca2+ than in its absence. Thus, it appears that a part of the epitope for the mAb described above is contained in the proposed Ca(2+)-binding site in the protease domain of human factor IX. This proposed site is analogous to the Ca(2+)-binding site in trypsin and elastase, and it may be involved in binding factor IXa to factor VIIIa.
Mismatch repair deficiency associated with complete remission to combination programmed cell death ligand immune therapy in a patient with sporadic urothelial carcinoma: immunotheranostic considerations (2015)

Clinicaltrials.gov NCT00938834. Registered 13 July 2009).
Interline CCD image sensor with an anti blooming structure (1982)

THE APPLICATION OF AN overflow drain and barrier positioned beside the photosensitive area1 has made it possible to suppress blooming of CCD image sensors. However, this method was found to sacrifice photosensitivity and dynamic range. This paper will describe an interline CCD sensor where the vertical overflow drain is positioned under, rather than beside the photodiode. Thus the cell area can now be used effectively for photoelectron generation and storage, and increased photosensitivity and dynamic range can be maintained. Furthermore, this technique eliminates the blooming phenomenon.
Production and Characteristics of Raw-Potato-Starch-Digesting α-Amylase from Bacillus subtilis 65 (1988)

A newly isolated bacterium, identified as Bacillus subtilis 65, was found to produce raw-starch-digesting alpha-amylase. The electrophoretically homogeneous preparation of enzyme (molecular weight, 68,000) digested and solubilized raw corn starch to glucose and maltose with small amounts of maltooligosaccharides ranging from maltotriose to maltoheptaose. This enzyme was different from other amylases and could digest raw potato starch almost as fast as it could corn starch, but it showed no adsorbability onto any kind of raw starch at any pH. The mixed preparation with Endomycopsis glucoamylase synergistically digested raw potato starch to glucose at 30 degrees C. The raw-potato-starch-digesting alpha-amylase showed strong digestibility to small substrates, which hydrolyzed maltotriose to maltose and glucose, and hydrolyzed p-nitrophenyl maltoside to p-nitrophenol and maltose, which is different from the capability of bacterial liquefying alpha-amylase.
Prognostic factors: Stage and receptor status in breast cancer (1992)

Hormone receptors add to the prognostic information provided by anatomic stage, but the contribution is insufficient to support a decision for or against systemic adjuvant therapy.
Beyond Watson and Crick: DNA Methylation and Molecular Enzymology of DNA Methyltransferases (2002)

DNA methyltransferases catalyze the transfer of a methyl group from S-adenosyl-L-methionine to cytosine or adenine bases in DNA. These enzymes challenge the Watson/Crick dogma in two instances: 1) They attach inheritable information to the DNA that is not encoded in the nucleotide sequence. This so-called epigenetic information has many important biological functions. In prokaryotes, DNA methylation is used to coordinate DNA replication and the cell cycle, to direct postreplicative mismatch repair, and to distinguish self and nonself DNA. In eukaryotes, DNA methylation contributes to the control of gene expression, the protection of the genome against selfish DNA, maintenance of genome integrity, parental imprinting, X-chromosome inactivation in mammals, and regulation of development. 2) The enzymatic mechanism of DNA methyltransferases is unusual, because these enzymes flip their target base out of the DNA helix and, thereby, locally disrupt the B-DNA helix. This review describes the biological functions of DNA methylation in bacteria, fungi, plants, and mammals. In addition, the structures and mechanisms of the DNA methyltransferases, which enable them to specifically recognize their DNA targets and to induce such large conformational changes of the DNA, are discussed.