gebhart/patrepeval huggingface dataset:
Synthesis of 6-Hydroxy-2-methyl-3-thioxo-2H-1,2,4-triazin-5-one (1996)

Abstract The title compound has been prepared in three steps from 2-methylthiosemicarbazide following acylation, cyclisation and cation exchange chromatography. It was fully characterised by the usual spectroscopic means as well as by 15N nmr spectroscopy and X-ray crystallographic analysis.
Expanded Instrument Comparison of Amplicon DNA Melting Analysis for Mutation Scanning and Genotyping (2007)

Different instruments vary widely in their ability to genotype homozygous variants and scan for heterozygotes by whole amplicon melting analysis. Instruments specifically designed for high-resolution melting, however, displayed the least variation, suggesting better genotyping accuracy and scanning sensitivity and specificity.
Phonon wave-packet dynamics at semiconductor interfaces by molecular-dynamics simulation (2002)

We directly observe phonon wave packets of well-defined frequency and polarization scattering at a coherent semiconductor interface using molecular-dynamics simulations. We find that in the low-frequency limit the transmission coefficients of both longitudinal and transverse acoustic phonons agree well with those predicted by the continuum-level based acoustic mismatch model. However, the transmission coefficients rapidly decrease close to the cutoff frequency, a result that can be understood within a simple one-dimensional discrete atomic-chain model. We also find that the transmission coefficient for transverse acoustic phonons depends strongly on the relative orientation of the polarization and the Si–Si bonds in the diamond lattice structure.
Therapeutic effects of 25-hydroxycholecalciferol and sodium etidronate on renal osteodystrophy. (1982)

The effects of long-term treatment with 25-hydroxycholecalciferol (25OHD3) and disodium ethane-1-hydroxydiphosphonate, or 25OHD3 alone on biochemical parameters, and radiographic and quantitative histomorphometry of bone tissue were evaluated in 17 dialysis patients. They all displayed evidence of bone disease consisting of osteitis fibrosa and defective mineralization of varying degree and predominance. 100 micrograms/day of 25OHD3 significantly improved the state of bone mineralization in many patients with a pronounced fall in the osteoid volume and surface and produced a small reduction in the active resorption surface. Serum parathyroid hormone (iPTH) and alkaline phosphatase levels decreased in some patients. The combination of 25OHD3 with EHDP caused the healing of bone mineralization as did 25OHD3 alone and produced a significant fall in serum alkaline phosphatase and iPTH. The mean magnitude of the reduction in iPTH was higher in patients treated with 25OHD3 and EHDP than with 25OHD3 alone. Treatment with 25OHD3 and EHDP seems more effective for the improvement of osteitis fibrosa than is 25OHD3 alone.
Molecular mechanisms of congenital hyperinsulinism (2015)

Congenital hyperinsulinism (CHI) is a complex heterogeneous condition in which insulin secretion from pancreatic β-cells is unregulated and inappropriate for the level of blood glucose. The inappropriate insulin secretion drives glucose into the insulin-sensitive tissues, such as the muscle, liver and adipose tissue, leading to severe hyperinsulinaemic hypoglycaemia (HH). At a molecular level, genetic abnormalities in nine different genes (ABCC8, KCNJ11, GLUD1, GCK, HNF4A, HNF1A, SLC16A1, UCP2 and HADH) have been identified which cause CHI. Autosomal recessive and dominant mutations in ABCC8/KCNJ11 are the commonest cause of medically unresponsive CHI. Mutations in GLUD1 and HADH lead to leucine-induced HH, and these two genes encode the key enzymes glutamate dehydrogenase and short chain 3-hydroxyacyl-CoA dehydrogenase which play a key role in amino acid and fatty acid regulation of insulin secretion respectively. Genetic abnormalities in HNF4A and HNF1A lead to a dual phenotype of HH in the newborn period and maturity onset-diabetes later in life. This state of the art review provides an update on the molecular basis of CHI.
Transforming Growth Factor β1 and Recruitment of Macrophages and Mast Cells in Airways in Chronic Obstructive Pulmonary Disease (1998)

Chronic airways inflammation is one of the features of chronic obstructive pulmonary disease (COPD). We demonstrated previously that bronchiolar epithelium in COPD contains increased numbers of macrophages and mast cells. Transforming growth factor beta1 (TGF-beta1) may be involved in this influx because it has chemotactic activity for macrophages and mast cells. In this study, we examined expression patterns of TGF-beta1, TGF-beta receptors type I and II (TGF-betaRI and TGF-betaRII) by immunohistochemistry and mRNA in situ hybridization in peripheral lung tissue of 14 current or ex-smokers with COPD (FEV1 < 75%) and 14 without COPD (FEV1 > 84%). In both groups, TGF-beta1 and its receptors are present in airway and alveolar epithelial cells, airway and vascular smooth muscle cells, and tissue and alveolar CD68(+) cells (considered herein to be macrophages). In subjects with COPD, a semiquantitative analysis revealed approximately twofold higher levels of TGF-beta1 mRNA and protein in bronchiolar and alveolar epithelium (p < 0.02) as compared with subjects without COPD. With regard to bronchiolar epithelial cells, we found a significant correlation between TGF-beta1 mRNA and protein expression (r = 0.62; p < 0.002), and between the FEV1 of all subjects together and TGF-beta1 protein (r = -0.60; p < 0.0002) and mRNA (r = -0.67; p < 0. 002) levels. The epithelial expression of TGF-beta1 mRNA and TGF-beta1 protein correlates with the number of intraepithelial macrophages (both: r = 0.44; p < 0.03) whereas intraepithelial mast cell numbers correlate with epithelial TGF-beta1 mRNA expression. These data suggest a role for TGF-beta1 in recruiting macrophages into the airway epithelium in COPD.
NADPH Oxidase Mediates Lipopolysaccharide-induced Neurotoxicity and Proinflammatory Gene Expression in Activated Microglia (2004)

Parkinson's disease is characterized by the progressive degeneration of dopaminergic neurons in the substantia nigra. We have previously reported that lipopolysaccharide (LPS)-induced degeneration of dopaminergic neurons is mediated by the release of proinflammatory factors from activated microglia. Here, we report the pivotal role of NADPH oxidase in inflammation-mediated neurotoxicity, where the LPS-induced loss of nigral dopaminergic neurons in vivo was significantly less pronounced in NADPH oxidase-deficient (PHOX-/-) mice when compared with control (PHOX+/+) mice. Dopaminergic neurons in primary mensencephalic neuron-glia cultures from PHOX+/+ mice were significantly more sensitive to LPS-induced neurotoxicity in vitro when compared with PHOX-/- mice. Further, PHOX+/+ neuron-glia cultures chemically depleted of microglia failed to show dopaminergic neurotoxicity with the addition of LPS. Neuron-enriched cultures from both PHOX+/+ mice and PHOX-/- mice also failed to show any direct LPS-induced dopaminergic neurotoxicity. However, the addition of PHOX+/+ microglia to neuron-enriched cultures from either strain resulted in reinstatement of LPS-induced dopaminergic neurotoxicity, supporting the role of microglia as the primary source of NADPH oxidase-generated insult and neurotoxicity. Immunostaining for F4/80 in mensencephalic neuron-glia cultures revealed that PHOX-/- microglia failed to show activated morphology at 10 h, suggesting an important role of reactive oxygen species (ROS) generated from NADPH oxidase in the early activation of microglia. LPS also failed to elicit extracellular superoxide and produced low levels of intracellular ROS in microglia-enriched cultures from PHOX-/- mice. Gene expression and release of tumor necrosis factor alpha was much lower in PHOX-/- mice than in control PHOX+/+ mice. Together, these results demonstrate the dual neurotoxic functions of microglial NADPH oxidase: 1) the production of extracellular ROS that is toxic to dopamine neurons and 2) the amplification of proinflammatory gene expression and associated neurotoxicity.
Bone Morphogenetic Proteins: From Basic Science to Clinical Applications (2001)

A.H. Reddi, PhD; Research Building 1, Room 2000, Center for Tissue Regeneration and Repair, Department of Orthopaedic Surgery, University of California-Davis School of Medicine, 4635 Second Avenue, Sacramento, CA 95817. E-mail address: [email protected]
A cell-culture reactor for the on-line evaluation of radiopharmaceuticals: evaluation of the lumped constant of FDG in human glioma cells. (2000)

The bioreactor represents an improved in vitro model for the on-line evaluation of radiotracers and combines a wide range of experimental setups and 3-dimensional, tissue-like cell cultivation with a technique for on-line radioactivity detection.
Crystal Structure of the Catalytic Domain of the PknB Serine/Threonine Kinase from Mycobacterium tuberculosis (2003)

With the advent of the sequencing programs of prokaryotic genomes, many examples of the presence of serine/threonine protein kinases in these organisms have been identified. Moreover, these kinases could be classified as homologues of those belonging to the well characterized superfamily of the eukaryotic serine/threonine and tyrosine kinases. Eleven such kinases were recognized in the genome of Mycobacterium tuberculosis. Here we report the crystal structure of an active form of PknB, one of the four M. tuberculosis kinases that are conserved in the downsized genome of Mycobacterium leprae and are therefore presumed to play an important role in the processes that regulate the complex life cycle of mycobacteria. Our structure confirms again the extraordinary conservation of the protein kinase fold and constitutes a landmark that extends this conservation across the evolutionary distance between high eukaryotes and eubacteria. The structure of PknB, in complex with a nucleotide triphosphate analog, reveals an enzyme in the active state with an unprecedented arrangement of the Gly-rich loop associated with a new conformation of the nucleotide gamma-phosphoryl group. It presents as well a partially disordered activation loop, suggesting an induced fit mode of binding for the so far unknown substrates of this kinase or for some modulating factor(s).
Carbonic Anhydrases An Overview (2008)

Carbonic anhydrases (CAs, EC 4.2.1.1) are widespread metalloenzymes all over the phylogenetic tree, with at least 4 distinct gene families encoding for them. At least 16 different alpha-CA isoforms were isolated in mammals, where these enzymes play crucial physiological roles. Representatives of the beta-delta-CA family are highly abundant in plants, diatoms, eubacteria and archaea. These enzymes are efficient catalysts for the reversible hydration of carbon dioxide to bicarbonate, but at least the alpha-CAs possess a high versatility, being able to catalyze different other hydrolytic processes The catalytic mechanism of the alpha-CAs is understood in detail: the active site consists of a Zn(II) ion co-ordinated by three histidine residues and a water molecule/hydroxide ion. The latter is the active species, acting as a potent nucleophile. For beta- and gamma-CAs, the zinc hydroxide mechanism is valid too, although at least some beta-class enzymes do not have water directly coordinated to the metal ion. CAs are inhibited by two classes of compounds: the metal complexing anions and the sulfonamides and their isosteres (sulfamates, sulfamides etc.) possessing the general formula RXSO(2)NH(2) (R = aryl; hetaryl; perhaloalkyl; X = nothing, O or NH). At least 25 clinically used drugs/agents in clinical development show applications as diuretics and antiglaucoma drugs, anticonvulsants, with some compounds being developed as anticancer agents/diagnostic tools for tumors, antiobesity agents, and antimicrobials/antifungals (inhibitors targeting CAs from pathogenic organisms such as Helicobacter pylori, Mycobacterium tuberculosis, Plasmodium falciparum, Candida albicans, etc). Several important physiological and physio-pathological functions are played by CA isozymes present in organisms all over the phylogenetic tree, related to respiration and transport of CO(2)/bicarbonate between metabolizing tissues and the lungs, pH and CO(2) homeostasis, electrolyte secretion in a variety of tissues/organs, biosynthetic reactions, such as the gluconeogenesis and ureagenesis among others (in animals), CO(2) fixation (in plants and algae), etc. The presence of these ubiquitous enzymes in so many tissues and in so different isoforms, represents an attractive goal for the design of inhibitors or activators with biomedical applications.
Complement proteins C5b-9 induce vesiculation of the endothelial plasma membrane and expose catalytic surface for assembly of the prothrombinase enzyme complex. (1990)

Assembly of the terminal complement proteins C5b-9 on human endothelial cells results in increased cytosolic calcium and nonlytic secretion of high molecular weight multimers of von Willebrand factor from intracellular storage granules. We now demonstrate that this C5b-9-induced secretory response is accompanied by vesiculation of membrane particles from the endothelial surface which express binding sites for factor Va and support prothrombinase activity. Exposure of factor Va binding sites after C5b-9 assembly was accompanied by greater than 2-fold increase in prothrombinase activity, which was not observed for cells exposed to C5b-8 (in the absence of C9). By contrast, only a 3-16% increase in prothrombinase activity was observed when these cells were maximally stimulated to secrete by either histamine, thrombin, or the Ca2+ ionophore A23187. Increased prothrombinase activity after C5b-9 was not accompanied by a change in thrombomodulin activity, and was unrelated to cell lysis, the complement-treated cells remaining greater than 99% viable. Endothelial prothrombinase activity was predominately associated with small membrane vesicles (less than 1 microns diameter) released from the cell monolayer. Analysis by fluorescence-gated flow cytometry revealed that these vesicles incorporate the C5b-9 proteins and express binding sites for factor Va. The capacity of the C5b-9 proteins to induce vesiculation of the endothelial plasma membrane and thereby expose catalytic surface for the prothrombinase enzyme complex may contribute to fibrin deposition associated with immune endothelial injury.
The NMDA Receptor Complex: A Promising Target for Novel Antiepileptic Strategies (2001)

Antiepileptic drugs (AEDs) cover a broad spectrum of pathological conditions ranging from seizures following congenital or acquired brain disorders to behavioural and psychiatric disorders and recently neuropathic pain. The need for novel antiepileptics raises from the expanding field of indications as well as from the fact, that special seizure types are refractory to common AEDs. In addition, many of the conventional antiepileptic drugs exhibit an unfavourable side-effect profile. Since there is growing evidence, that NMDA receptor activation might play a crucial role in epilepsy, NMDA receptor antagonists have become compounds of interest in preventing and treating seizures. This review focuses on NMDA receptor antagonistic compounds, which are already in use for the treatment of epileptic seizures (i. e. MgSO4, felbamate) and compounds in clinical trials (i. e. remacemide, ADCI). Further interest is put on NMDA antagonists in preclinical and biological testing (memantine, dizocilpine, conantokins, Co101244/PD174494, ifenprodil, arcaine, L-701,324, eliprodil, CGP40116, LY235959, LY233053, MRZ2/576, LU73068, 4-Cl-KYN). Some of the latter compounds are predominantely of academic interest (i. e. 4-Cl-KYN), others (i. e. dizocilpine, LY235959, LY233053) might be of therapeutical value when combined with conventional AEDs. In order to reduce adverse effects in antiepileptic medication using NMDA antagonists, special interest will be focused on subtype selective compounds. In this respect, Co101244, a novel potent and selective NR1/2B NMDA receptor antagonist might be a lead for therapeutically promising compounds.
The cepstrum: A guide to processing (1977)

This paper is a pragmatic tutorial review of the cepstrum literature focusing on data processing. The power, complex, and phase cepstra are shown to be easily related to one another. Problems associated with phase unwrapping, linear phase components, spectrum notching, aliasing, oversampling, and extending the data sequence with zeros are discussed. The advantages and disadvantages of windowing the sampled data sequence, the log spectrum, and the complex cepstrum are presented. The influence of noise upon the data processing procedures is discussed throughout the paper, but is not thoroughly analyzed. The effects of various forms of liftering the cepstrum are described. The results obtained by applying whitening and trend removal techniques to the spectrum prior to the calculation of the cepstrum are discussed. We have attempted to synthesize the results, procedures, and information peculiar to the many fields that are finding cepstrum analysis useful. In particular we discuss the interpretation and processing of data in such areas as speech, seismology, and hydroacoustics. But we must caution the reader that the paper is heavily influenced by our own experiences; specific procedures that have been found useful in one field should not be considered as totally general to other fields. It is hoped that this review will be of value to those familiar with the field and reduce the time required for those wishing to become so.
High-Throughput Middle-Down Analysis Using an Orbitrap (2010)

This report demonstrates the application of a capillary LC-LTQ-orbitrap system to provide automated middle-down analysis of proteolytic peptides in the mass range 3000 to 10,000 Da. The novel workflow combines an underutilized method in the orbitrap-high resolution, mass-accurate product ion measurements-with software tailored to search such data (ProSightPC 2.0) and an Asp-selective chemical cleavage approach that generates peptides across an extended mass range. The strategy using high resolution mass measurements on both precursor and product ions is analogous to that widely used on FT-ICR analyzers. The approach is demonstrated in an analysis of the highly basic ribosomal proteome isolated from human MCF7 cancer cells.
Genetics and the environment converge to dysregulate N-glycosylation in multiple sclerosis (2011)

How environmental factors combine with genetic risk at the molecular level to promote complex trait diseases such as multiple sclerosis (MS) is largely unknown. In mice, N-glycan branching by the Golgi enzymes Mgat1 and/or Mgat5 prevents T cell hyperactivity, cytotoxic T-lymphocyte antigen 4 (CTLA-4) endocytosis, spontaneous inflammatory demyelination and neurodegeneration, the latter pathologies characteristic of MS. Here we show that MS risk modulators converge to alter N-glycosylation and/or CTLA-4 surface retention conditional on metabolism and vitamin D(3), including genetic variants in interleukin-7 receptor-α (IL7RA*C), interleukin-2 receptor-α (IL2RA*T), MGAT1 (IV(A)V(T-T)) and CTLA-4 (Thr17Ala). Downregulation of Mgat1 by IL7RA*C and IL2RA*T is opposed by MGAT1 (IV(A)V(T-T)) and vitamin D(3), optimizing branching and mitigating MS risk when combined with enhanced CTLA-4 N-glycosylation by CTLA-4 Thr17. Our data suggest a molecular mechanism in MS whereby multiple environmental and genetic inputs lead to dysregulation of a final common pathway, namely N-glycosylation.
Insecurity of position-based quantum-cryptography protocols against entanglement attacks (2011)

Recently, position-based quantum cryptography has been claimed to be unconditionally secure. On the contrary, here we show that the existing proposals for position-based quantum cryptography are, in fact, insecure if entanglement is shared among two adversaries. Specifically, we demonstrate how the adversaries can incorporate ideas of quantum teleportation and quantum secret sharing to compromise the security with certainty. The common flaw to all current protocols is that the Pauli operators always map a codeword to a codeword (up to an irrelevant overall phase). We propose a modified scheme lacking this property in which the same cheating strategy used to undermine the previous protocols can succeed with a rate of at most $85%$. We prove the modified protocol is secure when the shared quantum resource between the adversaries is a two- or three-level system.
On Human Motion Prediction Using Recurrent Neural Networks (2017)

Human motion modelling is a classical problem at the intersection of graphics and computer vision, with applications spanning human-computer interaction, motion synthesis, and motion prediction for virtual and augmented reality. Following the success of deep learning methods in several computer vision tasks, recent work has focused on using deep recurrent neural networks (RNNs) to model human motion, with the goal of learning time-dependent representations that perform tasks such as short-term motion prediction and long-term human motion synthesis. We examine recent work, with a focus on the evaluation methodologies commonly used in the literature, and show that, surprisingly, state of the art performance can be achieved by a simple baseline that does not attempt to model motion at all. We investigate this result, and analyze recent RNN methods by looking at the architectures, loss functions, and training procedures used in state-of-the-art approaches. We propose three changes to the standard RNN models typically used for human motion, which results in a simple and scalable RNN architecture that obtains state-of-the-art performance on human motion prediction.
Cytotoxic effects of folate antagonists against methotrexate-resistant human leukemic lymphoblast CCRF-CEM cell lines. (1985)

A human T-lymphoblast cell line, CCRF-CEM/R1, resistant to methotrexate by virtue of increased dihydrofolate reductase activity, was grown in stepwise increasing concentrations of methotrexate. This additional selection pressure resulted in a cell line, CCRF-CEM/R2, resistant to methotrexate by virtue of both an elevation of dihydrofolate reductase activity and a marked decrease in methotrexate transport. The R1 and R2 cells were approximately 70- and 350-fold more resistant to methotrexate than were the parent cells. The effects of three folate antagonists were studied on these cell lines and also on CCRF-CEM/R3 cells, characterized by impaired methotrexate transport but normal levels of dihydrofolate reductase. The elevated reductase subline CCRF-CEM/R1 was cross-resistant to triazinate [Baker's antifol, NSC 139105; ethanesulfonic acid compounded with alpha-(2-chloro-4-[4,6-diamino-2,2-dimethyl-S-triazine-1-(2H)-yl] phenoxyl)-N,N-dimethyl-m-toluamide (1:1)] and trimetrexate (NSC 249008, JB-11, TMQ; 2,4-diamino-6-[(3,4,5-trimethoxyanilino)methyl]quinazoline), two nonclassical folate antagonists. In contrast, the transport defective subline, CCRF-CEM/R3 was not cross-resistant to these two compounds. In cells resistant to MTX by virtue of both mechanisms, CCRF-CEM/R2, triazinate, and trimetrexate were partially cross-resistant. All three methotrexate-resistant sublines showed minor cross-resistance to isoaminohydroxyquinazoline (IAHQ, NSC 289517; 5,8-dideazaisopteroylglutamate), a folate antagonist inhibitor of thymidylate synthase. These data demonstrate that methotrexate-resistant tumor cells may be effectively inhibited by antifolates with different route of entry into cells or with different enzyme targets.