gebhart/patrepeval huggingface dataset:
Synthesis of Releasable Electrophore Tags for Applications in Mass Spectrometry (2002)

Releasable electrophore mass tags (electrophore tags) are compounds for use as labels in ligand assays such as hybridization assays and immunoassays. In such assays, the electrophore-tagged reagent (e.g., DNA probe or antibody) is quantified at the conclusion of the assay by cleaving a bond in the attached tag so that the electrophore part can be brought into the gas phase (usually thermally) for detection by electron capture mass spectrometry (EC-MS) or a related technique. Interest in these tags is promoted mainly by their potential to provide highly sensitive and multiplexed assays. The high multiplexing arises from the opportunity to measure many such tags simultaneously in the mass spectrometer, where each tag has an electrophore part with a unique mass. In this study five precursors of electrophore mass tags are presented. Each precursor can lead to a large library of electrophore tags in a practical way, since each precursor can be converted to many different electrophore tags by reaction with commonly available phenols that provide a variation in mass. The phenol-reactive part of the tag is either a polyfluorobiphenyl or a benzyl chloride moiety. Representative library compounds are prepared and detected in an inert ester form by gas chromatography electron capture mass spectrometry (GC-EC-MS). Further, one tag is conjugated to DNA, and the resulting product is detected by laser-induced electron capture time-of-flight mass spectrometry on a silver surface. A calculation by the semiempirical method AM1 for an ion formed by one of the electrophores suggests that ring rotation promotes dissociative electron capture. The features of practical synthesis, simple composition, physicochemical stability, high multiplicity, high sensitivity, and potential for high throughput detection make releasable electrophore mass tags attractive for highly multiplexed assays. This includes their use in SNP assays or dideoxy DNA sequencing for detection of mutations in individuals, where the combination of high accuracy and speed is essential.
Metamaterials-based Salisbury screens with reduced angular sensitivity (2014)

We demonstrate that the incorporation of nonlocal nanowire metamaterials into Salisbury screens allows for a substantial reduction of the dependence of incident angle on the absorption maximum. Realizations of angle-independent Salisbury screens for the near-IR, mid-IR, and GHz frequencies are proposed and their performances are analyzed analytically and numerically. It is shown that nonlocal effective medium theory adequately describes the angular dependence of nanowire-based Salisbury screens.
Stereomutation of Pentavalent Compounds: Validating the Berry Pseudorotation, Redressing Ugi’s Turnstile Rotation, and Revealing the Two- and Three-Arm Turnstiles (2010)

A general reaction mechanism describes the qualitative change in chemical topology along the reaction pathway. On the basis of this principle, we present a method to characterize intramolecular substituent permutation in pentavalent compounds. A full description of the geometry around five-coordinate atoms using internal coordinates enables the analysis of the structural changes along the stereomutational intrinsic reaction coordinate. The fluxional behavior of experimentally known pentavalent phosphoranes, silicates, and transition-metal complexes has been investigated by density functional theory calculations, and three principal mechanisms have been identified: Berry pseudorotation, threefold cyclic permutation, and half-twist axial-equatorial interchange. The frequently cited turnstile rotation is shown to be equivalent to the Berry pseudorotation. In combination with graph theory, this approach provides a means to systematically investigate the stereomutation of pentavalent molecules and potentially identify hitherto-unknown mechanisms.
Research on prediction technique of network situation awareness (2008)

In this paper we study on the prediction technique of network situation awareness. It has two levels: the high-level situation and the low-level next attack step. The first one includes the indexes and the evaluation results of the network security situation, they are figure form, we use the RBF network to predict them for RBF’s self-learning character. Then we use the weighted attack graph to predict the next attack step. The weights represent the probability; the biggest weights indicate the most possible next attack step. The simulations show these prediction methods can offer different prediction capability to satisfy the prediction need of the network situation awareness.
Inducible UDP-glucose dehydrogenase from French bean (Phaseolus vulgaris L.) locates to vascular tissue and has alcohol dehydrogenase activity (1996)

UDP-glucose dehydrogenase is responsible for channelling UDP-glucose into the pool of UDP-sugars utilized in the synthesis of wall matrix polysaccharides and glycoproteins. It has been purified to homogeneity from suspension-cultured cells of French bean by a combination of hydrophobic-interaction chromatography, gel filtration and dye-ligand chromatography. The enzyme had a subunit of Mr 40,000. Km values were measured for UDP-glucose as 5.5 +/- 1.4 mM and for NAD+ as 20 +/- 3 microM. It was subject to inhibition by UDP-xylose. UDP-glucose dehydrogenase activity co-purified with alcohol dehydrogenase activity from suspension-cultured cells, elicitor-treated cells and elongating hypocotyls, even when many additional chromatographic steps were employed subsequently. The protein from each source was resolved into virtually identical patterns of isoforms on two-dimensional isoelectric focusing/PAGE. However, a combination of peptide mapping and sequence analysis, gel analysis using activity staining and kinetic analysis suggests that both activities are a function of the same protein. An antibody was raised and used to immunolocalize UDP-glucose dehydrogenase to developing xylem and phloem of French bean hypocotyl. Together with data published previously, these results are consistent with an important role in the regulation of carbon flux into wall matrix polysaccharides.
Cancer: Principles and Practice of Oncology. (1991)

Part I: Molecular Biology of Cancer Molecular Methods in Oncology Section 1. Amplification Techniques Section 2. RNA Interference Section 3. cDNA arrays Section 4. Tissue arrays Section 5. Cytogenetics Section 6. Bioinformatics Genomics and Proteomics Molecular Targets in Oncology Section 1. Signal transduction systems Section 2. Cell cycle Section 3. Apoptosis Section 4. Telomerase Invasion and Metastases Angiogenesis Cancer Immunology Part II: Principles of Oncology Etiology of Cancer: Viruses Section 1. RNA Viruses Section 2. DNA Viruses Etiology of Cancer: Chemical Factors Etiology of Cancer: Tobacco Etiology of Cancer: Physical Factors Epidemiology of Cancer Section 1. Epidemiologic Methods Section 2. Cancer Statistics Principles of Surgical Oncology Section 1. General Issues Section 2. Laparascopic Surgery Principles of Radiation Oncology Principles of Medical Oncology Pharmacology of Cancer Chemotherapy Section 2. Pharmocokinetics Section 3. Pharmacogenomics Section 4. Alkylating Agents Section 5. Cisplatin and its Analogues Section 6. Antimetabolites Section 7. Topoisomerase Interactive Agents Section 8. Antimicrotubule Agents Section 9. Miscellaneous Chemotherapeutic Agents Pharmacology of Cancer Biotherapeutics Section 1. Interferon Section 2. Interleukin 2 Section 3. Histone deacetylase inhibitors as differentiation agents Section 4. Monoclonal Antibodies Pharmacology of Endocrine Manipulation Design and Analysis of Clinical Trials Part III: Practice of Oncology Cancer Prevention: Preventing Tobacco-Related Cancers Cancer Prevention: Diet and Chemopreventive Agents Section 1. Dietary fat Section 2. Dietary Fiber Section 3. Dietary fruits and vegetables: naturally occurring anticarcinogens Section 4. Retinoids, carotenoids and micronutrients Section 5. Dietary Carcinogens Section 6. Cyclo-oxygenase inhibitors Section 7. Physical Activity and Body Weight Cancer Prevention: Role of Surgery in Cancer Prevention Cancer Screening Advanced Molecular Diagnostics Advanced Imaging Methods Section 1. Functional and Metabolic Imaging Section 2. Interventional Radiology Cancer Diagnosis: Endoscopy Section 1. Gastrointestinal endoscopy Section 2. Respiratory Tract Cancer of the Head and Neck Section 1. Molecular Biology of Head and Neck Tumors Section 2. Treatment of Head and Neck Cancers Section 3. Rehabilitation after Treatment for Head Cancer of the Lung Section 1. Molecular Biology of Lung Cancer Section 2. Non-small Cell Lung Cancer Section 3. Small Cell Lung Cancer Neoplasms of the Mediastinum Cancers of the Gastrointestinal Tract
HTF9C gene of 22q11.21 region associates with schizophrenia having deficit-sustained attention (2007)

SNP rs1633445 of the HTF9C gene may be associated with a deficit in sustained attention within schizophrenia, in a Taiwanese cohort. The deficit of sustained attention may be an endophenotype of schizophrenia, and warrants further study.
Use of herpes simplex virus and pseudorabies virus chimeric glycoprotein D molecules to identify regions critical for membrane fusion (2004)

Membrane fusion induced by herpes simplex virus (HSV) requires the action of four viral membrane glycoproteins (gB, gD, gH, and gL) and the binding of gD to one of its receptors, such as the herpesvirus entry mediator or nectin-1. The related animal herpesvirus, pseudorabies virus (PRV), encodes a homologous set of glycoproteins and its gD can also use nectin-1 as an entry receptor. We show here that PRV gD, when coexpressed with HSV gB, gH, and gL, cannot substitute for HSV gD in inducing fusion with target cells expressing nectin-1. Chimeric gD molecules composed of HSV and PRV sequences can substitute, provided the first 285 aa are from HSV gD. Because the first 261 aa were sufficient for receptor binding, this suggested that amino acids 262-285 contain a region required for cell fusion but not for receptor binding. Deletions from amino acids 250-299 failed to identify a specific subregion critical for cell fusion, except possibly for amino acids 250-255, which also influenced receptor binding. Instead, presence of a flexible stalk between the membrane and receptor-binding domain appears to be required, perhaps to enable conformational changes in gD on receptor binding and subsequent interactions of undefined regions of gD with the other glycoproteins required for membrane fusion.
Post-Translational Modifications of the TAK1-TAB Complex (2017)

Transforming growth factor-β (TGF-β)-activated kinase 1 (TAK1) is a member of the mitogen-activated protein kinase kinase kinase (MAPKKK) family that is activated by growth factors and cytokines such as TGF-β, IL-1β, and TNF-α, and mediates a wide range of biological processes through activation of the nuclear factor-κB (NF-κB) and the mitogen-activated protein (MAP) kinase signaling pathways. It is well established that activation status of TAK1 is tightly regulated by forming a complex with its binding partners, TAK1-binding proteins (TAB1, TAB2, and TAB3). Interestingly, recent evidence indicates the importance of post-translational modifications (PTMs) of TAK1 and TABs in the regulation of TAK1 activation. To date, a number of PTMs of TAK1 and TABs have been revealed, and these PTMs appear to fine-tune and coordinate TAK1 activities depending on the cellular context. This review therefore focuses on recent advances in the understanding of the PTMs of the TAK1-TAB complex.
Phenoxodiol, an anticancer isoflavene, induces immunomodulatory effects in vitro and in vivo (2009)

Phenoxodiol (PXD) is a synthetic analogue of the plant isoflavone genistein with improved anticancer efficacy. Various properties and mechanisms of action have been attributed to the drug, the most important being its ability to sensitize resistant tumour cells to chemotherapy, which led to its fast track FDA approval for phase II/III clinical trials. In this study, we examined the effects of PXD on human peripheral blood mononuclear cells (PBMC) and its potential role in regulating immune responses. We show that PXD, at concentrations >or=1 microg/ml (4 microM), inhibited proliferation and reduced the viability of healthy donor-derived PBMC. In contrast, lower PXD concentrations (0.05-0.5 microg/ml) augmented, upon 3-day incubation, PBMC cytotoxicity. Experiments with purified CD56(+) lymphocytes revealed that PXD enhanced the lytic function of natural killer (NK) cells by directly stimulating this lymphocytic subpopulation. Furthermore, in an in vivo colon cancer model, Balb/C mice administered low-dose PXD, exhibited significantly reduced tumour growth rates and prolonged survival (in 40% of the animals). Ex vivo results showed that PXD stimulated both NK and tumour-specific cell lytic activity. We conclude that PXD, when administered at low concentrations, can act as an immunomodulator, enhancing impaired immune responses, often seen in cancer-bearing individuals.
Molecular effect of FadD on the regulation and metabolism of fatty acid inEscherichia coli (2006)

Wild-type Escherichia coli can utilize exogenous long-chain fatty acids (C>12) as a sole carbon source for growth, but it cannot grow on medium-chain fatty acids. However, when the fadD gene from E. coli MG1655 was expressed in E. coli DH5alpha, the latter strain was found to utilize medium-chain fatty acids as its sole carbon source. Various E. coli strains thought to carry subtly different FadR phenotypes were all confirmed as using medium-chain fatty acids as their sole carbon source when the additional fadD was expressed. Semi-quantitative reverse transcription PCR analysis showed that the additional expression of fadD in E. coli strongly induced the expression of both fadE and fadBA. Excessive amounts of medium-chain acyl-CoA would probably bind to FadR and remove the inhibition of fatty acid beta-oxidation.
Mammalian Cdk5 is a functional homologue of the budding yeast Pho85 cyclin-dependent protein kinase (1999)

Mammalian Cdk5 is a member of the cyclin-dependent kinase family that is activated by a neuron-specific regulator, p35, to regulate neuronal migration and neurite outgrowth. p35/Cdk5 kinase colocalizes with and regulates the activity of the Pak1 kinase in neuronal growth cones and likely impacts on actin cytoskeletal dynamics through Pak1. Here, we describe a functional homologue of Cdk5 in budding yeast, Pho85. Like Cdk5, Pho85 has been implicated in actin cytoskeleton regulation through phosphorylation of an actin-regulatory protein. Overexpression of CDK5 in yeast cells complemented most phenotypes associated with pho85Delta, including defects in the repression of acid phosphatase expression, sensitivity to salt, and a G(1) progression defect. Consistent with the functional complementation, Cdk5 associated with and was activated by the Pho85 cyclins Pho80 and Pcl2 in yeast cells. In a reciprocal series of experiments, we found that Pho85 associated with the Cdk5 activators p35 and p25 to form an active kinase complex in mammalian and insect cells, supporting our hypothesis that Pho85 and Cdk5 are functionally related. Our results suggest the existence of a functionally conserved pathway involving Cdks and actin-regulatory proteins that promotes reorganization of the actin cytoskeleton in response to regulatory signals.
Chromosome localization of two human serine protease genes to region 14q11.2→q12 by in situ hybridization (1990)

Two human serine protease genes have been cloned. One corresponds to CTLA1, the human equivalent of the mouse cytotoxic cell protease gene Ctla-1, and the other is novel. Both genes were localized to 14q11.2----q12 by in situ hybridization. This result confirms the assignment of human CTLA1 to 14q11.2----q12 and provides new mapping data for another human serine protease gene located in the same chromosome region.
Accuracy and precision of two in-shoe pressure measurement systems (2002)

The recent rapid adoption of insole pressure measurement systems for clinical and ergonomic evaluations of human gait has necessitated a comprehensive understanding of the accuracy and precision of such systems. Five bench experiments were performed to examine the Pedar and F-Scan in-shoe pressure measurement systems. The insoles examined were the Pedar Y-sized right insole and the F-scan insole trimmed to the size and shape of a Pedar Y-sized insole. Data were sampled at 50 Hz at different levels of applied pressure, calibration procedure, duration of pressure application, insole age of use and experiment day or week. The system accuracy was determined by the per cent error of measurement, the system precision by the 95% tolerance interval of the per cent error. The results show that system accuracy and precision varied among levels of applied pressure, calibration procedure, duration of pressure application and insole age of use. The Pedar system showed the greatest accuracy and precision when the insole was new and measurements were taken (1) after a system calibration as specified by the manufacturer, (2) in the 50 - 500 kPa pressure range and (3) within a few seconds after pressure was applied. Under this condition, the measurement error was in the range -0.6 to 2.7%, and the magnitude (upper bound minus lower bound) of the 95% tolerance intervals was from 13.5 to 18.7%. Measuring less than 35 kPa with the Pedar system is not recommended. To ensure the accuracy and precision of the F-Scan system, users are recommended to estimate the range of the applied pressure and then choose a similar pressure level for calibration. Under this condition, the measurement error was in the range 1.3 - 5.8% and the magnitude (upper bound minus lower bound) of the 95% tolerance intervals was estimated to be in the range 1.1 - 14.8%. When the calibration pressure was outside this range of applied pressure, the per cent errors were considerably higher, ranging from -26.3 to 33.9%.
Brief interventions to prevent recurrence and alcohol-related problems in young adults admitted to the emergency ward following an alcohol-related event: a systematic review (2015)

The evidence is inconclusive, but the most effective interventions include at least one therapeutic contact several days after the event. Further research should provide more guidance about effective interventions in this age-group as well as about ways to favour delayed attendance for treatment. The potential role of parents or peers in supporting treatment also warrants further attention.
The α3 domain of major histocompatibility complex class I molecules plays a critical role in cytotoxic T lymphocyte stimulation (1989)

Allogeneic major histocompatibility complex class I molecules induce strong cytotoxic T lymphocyte (CTL) responses whereas xenogeneic molecules do not. We have tested a series of mouse/human hybrid molecules for their ability to stimulate mouse CTL. The molecules with murine alpha 3 domains consistently stimulated stronger CTL responses than those with human alpha 3 domains, independent of the species origin of the N-terminal alpha 1 or alpha 2 domains. We have found that the ability of class I molecules to induce strong cytotoxic responses correlates positively with their ability to stimulate expansion of the CD8+CD4-T cell subset. The results indicate that mouse T cells can recognize class I molecules with human alpha 1 and/or alpha 2 domains, but for efficient stimulation of these T cells it is important that the immunizing molecule contains a murine alpha 3 domain. We suggest that T cell priming requires an efficient interaction of CD8 with the class I alpha 3 domain, and this shows some species restriction.
Detection and quantitation of low numbers of chromosomes containing bcl-2 oncogene translocations using semi-nested PCR. (1994)

A PCR assay has been optimized for the detection of one or a few molecules of a translocation-containing human DNA sequence in the presence of a vast excess (7 micrograms) of the normal human genome. This procedure avoids blot hybridization by the use of two rounds of PCR with 20-22 cycles of amplification per round and by the replacement of one of the two primers from the first round of PCR with a different primer in the second round (semi-nested PCR). We demonstrate that very low numbers of the target DNA molecules can be quantitated by this semi-nested PCR. This method can be used to detect a single DNA molecule from one mutant cell displaying a translocation between the bcl-2 proto-oncogene region and a JH immunoglobulin gene sequence [t(14;18)] in a background of normal human DNA from 10(6) cells.
Protective Effects of Scutellarin and Breviscapine on Brain and Heart Ischemia in Rats (2007)

Scutellarin is an active molecule existing in Erigeron breviscapus (vant.) Hand-Mazz. The present work was designed to study the antiischemic effects of scutellarin and its mixture with another substance, breviscapine, in male Sprague-Dawley (SD) rats. Ligature of left anterior descending arteries was performed to induce acute myocardial infarction (MI), and the middle cerebral artery occlusion was created to induce focal cerebral ischemia. The MI size was significantly reduced by scutellarin (15 and 50 mg/kg) but not by breviscapine (5 to 50 mg/kg); the effect of scutellarin on the anti-MI was dose-dependent. Compared with control group, scutellarin (50 mg/kg) reduced the myocardium cell apoptosis in MI rats. The two drugs together (5 to 50 mg/kg) significantly reduced infarction size in focal brain ischemic rats (P < 0.05). There were no significant differences among the 3 dosages in breviscapine-treated rats, and the effect of scutellarin on the anticerebral ischemia was dose-dependent. The results demonstrate that the protective effects of scutellarin on cardiovascular and cerebrovascular ischemia were better than its mixture, breviscapine, in rats.
The HHpred interactive server for protein homology detection and structure prediction (2005)

HHpred is a fast server for remote protein homology detection and structure prediction and is the first to implement pairwise comparison of profile hidden Markov models (HMMs). It allows to search a wide choice of databases, such as the PDB, SCOP, Pfam, SMART, COGs and CDD. It accepts a single query sequence or a multiple alignment as input. Within only a few minutes it returns the search results in a user-friendly format similar to that of PSI-BLAST. Search options include local or global alignment and scoring secondary structure similarity. HHpred can produce pairwise query-template alignments, multiple alignments of the query with a set of templates selected from the search results, as well as 3D structural models that are calculated by the MODELLER software from these alignments. A detailed help facility is available. As a demonstration, we analyze the sequence of SpoVT, a transcriptional regulator from Bacillus subtilis. HHpred can be accessed at http://protevo.eb.tuebingen.mpg.de/hhpred.