gebhart/patrepeval huggingface dataset:
Sites of Reaction of the Gastric H,K-ATPase with Extracytoplasmic Thiol Reagents (1997)

The vesicular gastric H,K-ATPase catalyzes an electroneutral H for K exchange allowing acidification of the intravesicular space. There is a total of 28 cysteines present in the alpha subunit of the gastric H,K-ATPase, of which 10 are found in the predicted transmembrane segments and their connecting loop, and 9 are present in the beta subunit, of which 6 are disulfide-linked. To determine which of these was accessible to extracytoplasmic attack, the enzyme was inhibited by four different substituted 2-pyridylmethylsulfinyl benzimidazoles, 5-methoxy-2-[(4-methoxy-3, 5-dimethyl-2-pyridyl)methylsulfinyl]-1H-benzimidazole (omeprazole), 2-[(4-trifluoroethoxy-3-methyl-2-pyridyl)methylsulfinyl]-1H-ben zimida zole (lansoprazole), 5-difluoromethoxy-2-[3, 4-methoxy-2-pyridyl)methylsulfinyl]-1H-benzimidazole (pantoprazole), and 2-[(4-(3-methoxypropoxy)-3-methyl)-2-pyridyl)methylsulfinyl]-1H-++ +benzi midazole (rabeprazole), under acid transporting conditions. All of these compounds are weak bases that accumulate in the acidic space generated by the pump and undergo an acid catalyzed rearrangement to a cationic sulfenamide, which forms disulfides with accessible cysteines. The relative rates of acid activation of these compounds corresponded to the relative rates of inhibition of ATPase activity and acid transport. Fragmentation of the enzyme by trypsin followed by SDS-polyacrylamide gel electrophoresis showed that omeprazole bound covalently to one of the two cysteines in the domains containing the fifth and sixth transmembrane segments and their extracytoplasmic loop and to cysteine 892 in the loop between the seventh and eighth transmembrane segments, but inhibition correlated with the reaction with cysteines in the fifth and sixth domain. Lansoprazole bound to the cysteines in these two domains as well as to cysteine 321 toward the extracytoplasmic end of the third transmembrane segments. Pantoprazole bound only to either cysteine 813 or 822 in the fifth and sixth transmembrane region. The inhibition of Rabeprazole correlated also with its binding to this part of the protein, but this compound continued to bind after full inhibition, eventually binding also to cysteines 321 and 892. No binding was found to any of the cysteines in the seventh to tenth transmembrane segments. Thermolysin digestion of the isolated omeprazole-labeled fifth and sixth transmembrane pair showed that cysteine 813 was the site of labeling. It is concluded that binding of these sided reagents to cysteine 813 in the loop between transmembrane (TM)5 and TM6 is sufficient for inhibition of ATPase activity and acid transport by the gastric acid pump. Of the 10 cysteines present in the membrane and extracytoplasmic domain, only three are exposed sufficiently to allow reactivity with these cationic thiol reagents. The binding to cysteine 813 defines the location of the extracytoplasmic loop between TM5 and TM6 and places the carboxylic acids 820 and 824 conserved between the gastric H,K- and the Na,K-ATPases in TM6, consistent with their assumed role in cation binding.
Multiple Novel Prostate Cancer Predisposition Loci Confirmed by an International Study: The PRACTICAL Consortium (2008)

A recent genome-wide association study found that genetic variants on chromosomes 3, 6, 7, 10, 11, 19 and X were associated with prostate cancer risk. We evaluated the most significant single-nucleotide polymorphisms (SNP) in these loci using a worldwide consortium of 13 groups (PRACTICAL). Blood DNA from 7,370 prostate cancer cases and 5,742 male controls was analyzed by genotyping assays. Odds ratios (OR) associated with each genotype were estimated using unconditional logistic regression. Six of the seven SNPs showed clear evidence of association with prostate cancer (P = 0.0007-P = 10(-17)). For each of these six SNPs, the estimated per-allele OR was similar to those previously reported and ranged from 1.12 to 1.29. One SNP on 3p12 (rs2660753) showed a weaker association than previously reported [per-allele OR, 1.08 (95% confidence interval, 1.00-1.16; P = 0.06) versus 1.18 (95% confidence interval, 1.06-1.31)]. The combined risks associated with each pair of SNPs were consistent with a multiplicative risk model. Under this model, and in combination with previously reported SNPs on 8q and 17q, these loci explain 16% of the familial risk of the disease, and men in the top 10% of the risk distribution have a 2.1-fold increased risk relative to general population rates. This study provides strong confirmation of these susceptibility loci in multiple populations and shows that they make an important contribution to prostate cancer risk prediction.
Mesenchymal Stem Cells: Mechanisms of Inflammation (2011)

In adults, human mesenchymal stem cells (hMSCs) are found in vivo at low frequency and are defined by their capacity to differentiate into bone, cartilage, and adipose tissue, depending on the stimuli and culture conditions under which they are expanded. Although MSCs were initially hypothesized to be the panacea for regenerating tissues, MSCs appear to be more important in therapeutics to regulate the immune response invoked in settings such as tissue injury, transplantation, and autoimmunity. MSCs have been used therapeutically in clinical trials and subsequently in practice to treat graft-versus-host disease following bone marrow transplantation. Reports of successful immune modulation suggest efficacy in a wide range of autoimmune conditions, such as demyelinating neurological disease (multiple sclerosis), systemic lupus erythematosus, and Crohn's disease, among others. This review provides background information about hMSCs and also describes their putative mechanisms of action in inflammation. We provide a summary of ongoing clinical trials to allow (a) full comprehension of the range of diseases in which hMSC therapy may be beneficial and (b) identification of gaps in our knowledge about the mechanisms of action of therapeutic MSCs in disease.
Development of a Practical Synthesis of DPP IV Inhibitor LY2497282 (2008)

A new synthetic route to LY2497282 (1), a potent and selective DPP IV inhibitor for the potential treatment of diabetes, suitable for the preparation of multikilogram quantities is described. The key step involved a stereoselective addition of the dianion of nicotinamide 8 to N-dibenzyl-protected α-amino aldehyde 12, which was derived from N-acetyl-protected amino ester 14 without epimerization. The desired Felkin-Anh nonchelation controlled anti-amino alcohol 11 was isolated with >99% HPLC area and >99% ee by crystallization. After removing the dibenzyl protecting group under transfer hydrogenation conditions, LY2497282 (1) was finally obtained in 39% overall yield with a six-step longest linear sequence starting from N-acetyl-protected amino ester 14.
Detection of clonal immunoglobulin gene rearrangements by polymerase chain reaction amplification and single-strand conformational polymorphism analysis. (1993)

Analysis of immunoglobulin gene rearrangements by Southern blotting is a sensitive and specific method for detecting B cell malignancies but requires a relatively large amount of intact DNA. It cannot be utilized in many cases where only a small amount of tissue is available or where the tissue has been fixed. This report demonstrates that polymerase chain reaction (PCR) amplification in conjunction with single-strand conformational polymorphism (SSCP) analysis can be utilized to detect clonal immunoglobulin heavy chain (IgH) gene rearrangements. IgH gene rearrangements from a series of frozen or formalin-fixed B cell malignancies were PCR-amplified using oligonucleotide primers, based upon consensus sequences in the IgH variable and joining regions. Analysis of the single-stranded PCR products on nondenaturing polyacrylamide gels revealed discrete SSCPs corresponding to the malignant B cells. These SSCPs were detectable when the malignant cells represented as few as 0.2% of the total mononuclear cells in peripheral blood. PCR amplification in conjunction with SSCP analysis thus provides a sensitive and specific method to detect clonal IgH rearrangements from minute amounts of fresh, frozen, or fixed tissue.
Effects of Repeated 20-Hz Electrical Stimulation on Functional Recovery Following Peripheral Nerve Injury (2019)

One hour of 20-Hz continuous electrical stimulation (ES) applied at the time of injury promotes the regeneration of axons in cut peripheral nerves. A more robust enhancement of peripheral axon regeneration is achieved by 2 weeks of daily treadmill exercise. We investigated whether repeated applications of brief ES (mES) would be more effective in promoting regeneration than a single application. Sciatic nerves of C57B6 mice were cut and repaired by end-to-end anastomosis. At that time and every third day for 2 weeks, the repaired nerve was stimulated for 1 hour at 20 Hz. In controls, injured mice were either untreated or treated with ES only once. Direct muscle responses recorded from reinnervated muscles in awake animals were observed earlier both in mice treated with ES and mES than untreated controls. Their amplitudes increased progressively over the post transection study period, but the rate of this progression was increased significantly only in animals treated once with ES. Monosynaptic H reflexes recovered to pretransection levels in both untreated and singly treated mice but in the animals treated repeatedly, they were maintained at more than twice that of the same reflexes recorded prior to injury. In anatomical analyses, both excitatory and inhibitory synaptic contacts with the cell bodies of injured motoneurons, including those expressing the vesicular glutamate transporter 1 (VGLUT1), were sustained in mice treated repeatedly but not in singly treated or untreated mice. Repeated ES does not enhance the rate of restoration of functional muscle reinnervation and results in the retention of exaggerated reflexes.
Transthyretin, Thyroxine, and Retinol-Binding Protein in Human Cerebrospinal Fluid: Effect of Lead Exposure (2001)

Transthyretin (TTR), synthesized by the choroid plexus, is proposed to have a role in transport of thyroid hormones in the brain. Our previous studies in animals suggest that sequestration of lead (Pb) in the choroid plexus may lead to a marked decrease in TTR levels in the cerebrospinal fluid (CSF). The objectives of this study were to establish in humans whether TTR and thyroxine (T(4)) are correlated in the CSF, and whether CSF levels of Pb are associated with those of TTR, T(4), and/or retinol-binding protein (RBP). Eighty-two paired CSF and blood/serum samples were collected from patients undergoing clinical diagnosis of CSF chemistry. Results showed that the mean value of CSF concentrations for TTR was 3.33 +/- 1.60 microg/mg of CSF proteins (mean +/- SD, n = 82), for total T(4) (TT(4)) was 1.56 +/- 1.68 ng/mg (n = 82), for RBP was 0.34 +/- 0.19 microg/mg (n = 82), and for Pb was 0.53 +/- 0.69 microg/dl (n = 61 for those above the detection limit). Linear regression analyses revealed that CSF TTR levels were positively associated with those of CSF TT(4) (r = 0.33, p < 0.005). CSF TTR concentrations, however, were inversely associated with CSF Pb concentrations (r = -0.29, p < 0.05). There was an inverse, albeit weak, correlation between CSF TT(4) and CSF Pb concentrations (r = -0.22, p = 0.09). The concentrations of TTR, TT(4), and Pb in the CSF did not vary as the function of their levels in blood or serum, but RBP concentrations in the CSF did correlate to those of serum (r = 0.39, p < 0.0005). Unlike TTR, CSF RBP concentrations were not influenced by PB: These human data are consistent with our earlier observations in animals, which suggest that TTR is required for thyroxine transport in the CSF and that Pb exposure is likely associated with diminished TTR levels in the CSF.
Enterprise-level architecture for interactive web-based 3D visualization of geo-referenced repositories (2009)

Interoperability, interactivity and 3D visualization are three of the most important challenges related to Geographical Information Systems. In the last few years, research on interoperability has evolved from simple exchange of spatial data files, through the establishment of standardized spatial data repositories, to the first initiatives allowing management of semantic aspects of data. Interoperability has been mainly hampered by the need to agree on standards, and to develop appropriate tools and methods. The Open Geospatial Consortium (OGC) has proposed a number of standards with the intention of promoting interoperability through the use of open services such as Web Mapping Service (WMS), Web Processing Service (WPS), Web Feature Service (WFS) and Web Coverage Service (WCS). However, there are a number of open issues regarding interactivity, 3D data visualization, fault tolerance, scalability, server-independent implementation, delayed-time transactions, to name but a few, that clearly reflect the need for further study and discussion. This paper presents a service-oriented architecture in the context of interoperable Web 3D GIS applications, designed to support features such as manipulation, processing and visual analysis of geographical information.
Generation of arbitrary quadrature signals using one dual-drive Modulator (2005)

Regardless of the number of constellation points, all quadrature-amplitude modulation (QAM) signals can be generated using a single dual-drive Mach-Zehnder modulator. When the general method is applied to quadrature-phase-shift-keying (QPSK) signals, three different QPSK transmitters are shown with drive signals having four, three, or two levels. The usage of only one dual-drive modulator greatly simplifies the design of QAM and QPSK transmitters.
Charon Phages: Safer Derivatives of Bacteriophage Lambda for DNA Cloning (1977)

The Charon lambda bacteriophages have been developed as vectors for cloning. Their construction incorporates mutations that make them simple to use and also greatly increases their safety for the biological containment of cloned recombinant DNA. Three of the Charon vector phages, 3A, 4A, and 16A, have been certified for use as EK2 vector-host systems, when propagated in bulk in a special bacterial host, DP50SupF. We present here some of the data on which the safety of these systems was evaluated. DNA fragments ranging in size from 0 to 2.2 X 10(4) base pairs can be cloned in these EK2 Charon phages.
FGFR2 mutation associated with clinical manifestations consistent with Antley-Bixler syndrome (1998)

The Antley-Bixler syndrome (ABS) is a rare syndrome with synostosis of cranial sutures and elbow joints as minimal diagnostic criteria. The inheritance has been suggested to be autosomal recessive based on two families with sib recurrence with both sexes being affected, and two cases born to consanguineous parents. We report the first case of ABS associated with an apparent dominant de novo mutation in the fibroblast growth factor receptor 2 (FGFR2) gene. The patient was found to be heterozygous for a C-->G transversion at nucleotide 1064, which predicts a Ser351Cys amino acid substitution in the IgIII domain of FGFR2. Apart from the craniosynostosis and elbow ankylosis, our patient also presented with severe spinal dysraphism, the first report of such a finding in association with ABS. This suggests that FGFR2 is expressed as early as the fourth week of embryogenesis when somite formation occurs. We propose that the Antley-Bixler syndrome is an autosomal dominant condition with possible gonadal mosaicism. Alternatively, there may be two types of ABS: an autosomal dominant form and an autosomal recessive form. In light of our findings, FGFR mutations should be looked for in other craniosynostosis patients with elbow synostosis.
Design Loading for Bulk Solid Containers (1991)

This paper provides an overview of the SAA Standard AS 3774 - Loads on Bulk Solid Containers. This overview will briefly trace the development, identify the scope and briefly describe container classification and geometry, bulk solid properties and main loads types considered in the Standard. In addition individual loads constituting the main load types are briefly covered. Particular emphasis is devoted to the determination of normal service loads and the basis of their evaluation procedure for content generated loads in symmetrically filled containers. Brief mention is also made to eccentrically filled and discharged containers and the additional load situations covered. The latter highlights the intended wide application of the Standard.
Characterization of mouse non-receptor tyrosine kinase gene, HYL. (1994)

We previously reported a novel human non-receptor tyrosine kinase gene, HYL (hematopoietic consensus tyrosine-lacking kinase) (Sakano et al., 1994), which consists of each of the SH2 (src homology 2), SH3 and tyrosine kinase catalytic domains. HYL has unique structural features shared with CSK (C-terminal Src kinase). Recently it has also been reported that matk (Bennett et al., 1994) and Ctk (Klages et al., 1994) are isolated as novel kinases with structural similarity to CSK. Comparisons of cDNA sequence indicate the HYL, matk and Ctk are the same gene. We further characterized the mouse HYL genomic structure and HYL mRNA expression in mouse brain. The mouse HYL gene is distributed over 5.8 kb and is composed of 12 exons. The exon-intron organization is almost identical with that of human CSK. The mouse HYL gene was assigned to the R-positive C1 band of chromosome 10 by fluorescent in situ hybridization. RNA in situ hybridization demonstrated the broad distribution of HYL mRNA expression in various neuronal cells. Especially, strong signals were detected in Purkinje cells, pyramidal cells in the hippocampus, granule cells in the dentate gyrus, and mitral cells in the olfactory bulb, indicating that mRNA expression of HYL in brain is very similar to that of SRC-family kinases. These findings establish close relationship between the HYL and CSK genes and also suggest that HYL may play an important role in signal transduction through SRC-family kinases in the central nervous system.
RNA-transfection of γ/δ T cells with a chimeric antigen receptor or an α/β T-cell receptor: a safer alternative to genetically engineered α/β T cells for the immunotherapy of melanoma (2017)

We present a protocol adaptable to GMP for the expansion of γ/δ T cells and their subsequent RNA-transfection with tumor-specific TCRs or CARs. Given the transient receptor expression, the reduced cytokine release, and the equivalent cytotoxicity, these γ/δ T cells may represent a safer complementation to genetically engineered conventional T cells in the immunotherapy of melanoma (Exper Dermatol 26: 157, 2017, J Investig Dermatol 136: A173, 2016).
Overexpression of CD1d by Keratinocytes in Psoriasis and CD1d-Dependent IFN-γ Production by NK-T Cells (2000)

The MHC class I-like protein CD1d is a nonpolymorphic molecule that plays a central role in development and activation of a subset of T cells that coexpress receptors used by NK cells (NK-T cells). Recently, T cells bearing NK receptors were identified in acute and chronic lesions of psoriasis. To determine whether NK-T cells could interact with epidermal cells, we examined the pattern of expression of CD1d in normal skin, psoriasis, and related skin disorders, using a panel of CD1d-specific mAbs. CD1d was expressed by keratinocytes in normal skin, although expression was at a relatively low level and was generally confined to upper level keratinocytes immediately beneath the lipid-rich stratum corneum. In contrast, there was overexpression of CD1d in chronic, active psoriatic plaques. CD1d could be rapidly induced on keratinocytes in normal skin by physical trauma that disrupted barrier function or by application of a potent contact-sensitizing agent. Keratinocytes displayed enhanced CD1d following exposure to IFN-gamma. Combining CD1d-positive keratinocytes with human NK-T cell clones resulted in clustering of NK-T cells, and while no significant proliferation ensued, NK-T cells became activated to produce large amounts of IFN-gamma. We conclude that CD1d can be expressed in a functionally active form by keratinocytes and is up-regulated in psoriasis and other inflammatory dermatoses. The ability of IFN-gamma to enhance keratinocyte CD1d expression and the subsequent ability of CD1d-positive keratinocytes to activate NK-T cells to produce IFN-gamma, could provide a mechanism that contributes to the pathogenesis of psoriasis and other skin disorders.
Brain Under Surveillance: The Microglia Patrol (2005)

The environment that cells encounter within tissues is extremely complex and virtually impossible to reconstitute in vitro. Two-photon microscopy on tissues of living animals is rapidly revealing the behavior of cells in their natural environment. In their Perspective,
 Fetler and Amigorena
 discuss two recent papers that use this powerful imaging technique to observe the dynamic behavior of microglial cells in a live mouse brain before and after brain injury.
Muscle satellite (stem) cell activation during local tissue injury and repair (2003)

In post-mitotic tissues, damaged cells are not replaced by new cells and hence effective local tissue repair mechanisms are required. In skeletal muscle, which is a syncytium, additional nuclei are obtained from muscle satellite (stem) cells that multiply and then fuse with the damaged fibres. Although insulin-like growth factor-I (IGF-l) had been previously implicated, it is now clear that muscle expresses at least two splice variants of the IGF-I gene: a mechanosensitive, autocrine, growth factor (MGF) and one that is similar to the liver type (IGF-IEa). To investigate this activation mechanism, local damage was induced by stretch combined with electrical stimulation or injection of bupivacaine in the rat anterior tibialis muscle and the time course of regeneration followed morphologically. Satellite cell activation was studied by the distribution and levels of expression of M-cadherin (M-cad) and related to the expression of the two forms of IGF-I. It was found that the following local damage MGF expression preceded that of M-cad whereas IGF-IEa peaked later than M-cad. The evidence suggests therefore that an initial pulse of MGF expression following damage is what activates the satellite cells and that this is followed by the later expression of IGF-IEa to maintain protein synthesis to complete the repair.
Anticandidal activity of pyrimidine-peptide conjugates (1980)

The ability of conjugates of peptides and 5-fluorocytosine or 5-fluoroorotic acid to enter Candida albicans was investigated. A number of conjugates of 5-fluoroorotic acid and peptides were synthesized using 1-(ethoxy-carbonyl)-2-ethoxy-1,2-dihydroquinoline as the coupling agent. Orotyl-L-leucyl-L-leucine, 5-fluoro-4-(N-succinamoyl-L-alanyl-L-leucine)-2(1H)-pyrimidinone [a 5-fluorocytosine derivative], and 5-fluoroorotyl-L-leucyl-L-leucine all inhibited the uptake of trimethionine into C. albicans WD 18-4. Inhibition by 5-fluoroorotyl-L-leucyl-L-leucine was competitive as judged using double-reciprocal plots. Evaluation of minimum inhibitory concentrations of peptide-5-fluorocytosine conjugates suggest that these conjugates enter C. albicans in the intact form. These results provide the first experimental evidence that peptides can carry pyrimidines into a eukaryote.
LVI.—Crystalline glycollic aldehyde (1899)

H. J. H. Fenton and H. Jackson, J. Chem. Soc., Trans., 1899, 75, 575 DOI: 10.1039/CT8997500575