gebhart/patrepeval huggingface dataset:
All individual domains of staphylococcal protein A show Fab binding (2006)

The interactions between the individual domains (E, D, A, B and C) of staphylococcal protein A (SPA) and Fc and Fab regions of human immunoglobulins were studied using real-time biospecific interaction analysis. An engineered domain Z, similar to fragment B but with a single glycine to alanine amino acid substitution, was also included in the study. The domains were expressed in Escherichia coli, affinity purified and immobilised onto sensor chip surfaces in a directed manner using a unique C-terminal cysteine residue engineered into the recombinant proteins. All domains bound to a recombinant human IgG1 Fc fragment with similar strength. For the first time, binding to human Fab was demonstrated for all native SPA domains, using both polyclonal F(ab')2 and a recombinant scFv fragment as reagents. Interestingly, the engineered Z domain showed a considerably lower affinity for Fab as compared to the native domains.
Post‐dural puncture syndrome in an elderly patient with remote history of previous post‐dural puncture syndrome (2002)

History of previous post-dural puncture syndrome (PDPS) is a strong risk factor for another PDPS when spinal anesthesia is readministered to these patients. We herein report a case to show that this general rule may still apply even after the passage of 50 years.
Crystal structure of human type II inosine monophosphate dehydrogenase: Implications for ligand binding and drug design (1999)

Inosine monophosphate dehydrogenase (IMPDH) controls a key metabolic step in the regulation of cell growth and differentiation. This step is the NAD-dependent oxidation of inosine 5' monophosphate (IMP) to xanthosine 5' monophosphate, the rate-limiting step in the synthesis of the guanine nucleotides. Two isoforms of IMPDH have been identified, one of which (type II) is significantly up- regulated in neoplastic and differentiating cells. As such, it has been identified as a major target in antitumor and immunosuppressive drug design. We present here the 2.9-A structure of a ternary complex of the human type II isoform of IMPDH. The complex contains the substrate analogue 6-chloropurine riboside 5'-monophosphate (6-Cl-IMP) and the NAD analogue selenazole-4-carboxamide adenine dinucleotide, the selenium derivative of the active metabolite of the antitumor drug tiazofurin. The enzyme forms a homotetramer, with the dinucleotide binding at the monomer-monomer interface. The 6 chloro-substituted purine base is dehalogenated, forming a covalent adduct at C6 with Cys-331. The dinucleotide selenazole base is stacked against the 6-Cl-IMP purine ring in an orientation consistent with the B-side stereochemistry of hydride transfer seen with NAD. The adenosine end of the ligand interacts with residues not conserved between the type I and type II isoforms, suggesting strategies for the design of isoform-specific agents.
E-Cadherin Engagement Stimulates Tyrosine Phosphorylation (1997)

Cadherins are cell adhesion molecules concentrated at intercellular adherens junctions, where they form a multiprotein complex with cytoplasmic catenins. Although cell-cell interactions affect many aspects of cell behavior, little is known about signaling pathways triggered by cadherin engagement. We show here that E-cadherin-mediated cell-cell adhesion leads to a rapid increase in tyrosine phosphorylation at sites of cell-cell contact and that this stimulation of tyrosine phosphorylation can be mimicked by aggregation of E-cadherin with antibodies. The proteins that become phosphorylated are distinct from those previously shown to be tyrosine phosphorylated in response to integrin-mediated adhesion and include ras-GAP. We also find that E-cadherin-mediated tyrosine phosphorylation is not required for the assembly of adherens-type junctions.
Glutathione-induced sodium currents in neocortex (1996)

The present report demonstrates that glutathione (GSH), a tripeptide composed of glutamate, glycine and cysteine (gamma-L-glutamyl-L-cysteinyl-glycine) and best known as a free radical scavenger, elicits a large fast depolarizing potential when applied to cortical slices. This potential is maximally larger than that produced by either NMDA or AMPA. Like AMPA, the GSH current appears to be carried by sodium ions, but cannot be blocked by the glutamate receptor antagonists AP5 or DNQX. In addition, removal of external calcium or blockade of potassium currents by TEA does not diminish the GSH-induced potential. Together, these results suggest that GSH acts through its own receptor-mediated channels, independently of the known EAA receptors, and that its receptors may be a key, and previously unknown, component of cortical excitatory neurotransmission.
MPS1: a small, evolutionarily conserved zinc finger protein from the protozoan Toxoplasma gondii (1999)

Within the expressed sequence tag (EST) dataset of Toxoplasma gondii we have identified several ESTs encoding a protein similar to the small zinc finger protein MPS1. In human it is suggested that MPS1 plays a role as a transcriptional mediator in response to various growth factors and it is used as a tumour marker in sera from cancer patients. However, in rat a cDNA sequence homologous to MPS1 encodes ribosomal protein S27. To further characterise MPS1 in T. gondii we transformed tachyzoites with a c-Myc-tagged version of the Toxoplasma MPS1 cDNA, flanked by SAG1 sequences. Western blot analysis showed that the Myc-MPS1 was only poorly expressed in the stable transformants. In contrast, Northern blot analysis demonstrated that the Myc-MPS1 mRNA was abundantly transcribed and that the endogenous level of MPS1 mRNA was not affected.
Chronic Actions of a Novel Oral B-Type Natriuretic Peptide Conjugate in Normal Dogs and Acute Actions in Angiotensin II–Mediated Hypertension (2008)

This study reports for the first time that a novel conjugated oral hBNP possesses blood pressure-lowering and natriuretic actions over a 6-day period in normal dogs. Furthermore, hBNP-054 activates cGMP and reduces MAP in a model of acute hypertension. These findings advance the concept that orally administered chronic BNP is a potential therapeutic strategy for cardiovascular diseases such as hypertension.
Liquid expanded-liquid condensed phase transition in Langmuir films of discotic molecules (1987)

We have measured the surface pressure isotherms of Langmuir monolayers of benzene-hexa-n-alkanoates (BH-n) spread at an air-water interface. These disc-like molecules are composed of six aliphatic chains attached to the central benzene nucleus by six ester bonds. The hydrophilic ester groups act as pinning points and hold the benzene nucleus flat on the water surface. For the lower homologs BH-5 to BH-7, we observe that the so-called liquid expanded phase obtained at high areas per molecule transforms into the liquid condensed phase upon lateral compression. The transition is approximately first-order, with a plateau region of finite slope and a single discontinuity in the monolayer compressibility. The associated heat of transition, as calculated from the Clapeyron equation, decreases linearly with temperature and extrapolates to zero at the critical temperature Tcrit. Above Tcrit, the transition disappears and the liquid expanded phase is observed at all areas per molecule. Contrary to the phospholipid and single chain fatty acid cases, T crit is found to decrease when the chain length increases. We interpret the phase change as an order-disorder transition of the aliphatic chains from a gauche to an all-trans conformation. Based on the areas per molecule occupied in each monolayer state, we can also infer that the chains get lifted up from an orientation parallel to an orientation vertical, relative to the interface.
A generalized series approach to MR spectroscopic imaging (1991)

The problem of precise spatial localization of spectral information in magnetic resonance (MR) spectroscopic imaging is addressed. A novel method, called GSLIM (generalized spectral location by imaging), is proposed to make possible the marriage of high-resolution proton imaging with spectroscopic imaging and localization. This method improves on the conventional Fourier series inversion method used in chemical shift imaging (CSI) and the compartmental modeling method used in SLIM by using a generalized series framework for optimal representation of the spectral function. In this way, a priori information extracted from proton imaging can be used, as in SLIM, and the robustness and data consistency of CSI are also retained. Simulation results show that GSLIM can significantly reduce spectral leakage in CSI and inhomogeneity errors in SLIM. It can also reveal compartmental inhomogeneities, and can easily be extended to handle other a priori constraints when necessary. This approach, with some further development, may achieve an optimal combination of sensitivity, quantitative accuracy, speed, and flexibility for in vivo spectroscopy.
Overview of the protein-protein interaction annotation extraction task of BioCreative II (2008)

The BioCreative II PPI task is the first attempt to compare the performance of text-mining tools specific for each of the basic steps of the PPI extraction pipeline. The challenges identified range from problems in full-text format conversion of articles to difficulties in detecting interactor protein pairs and then linking them to their database records. Some limitations were also encountered when using a single (and possibly incomplete) reference database for protein normalization or when limiting search for interactor proteins to co-occurrence within a single sentence, when a mention might span neighboring sentences. Finally, distinguishing between novel, experimentally verified interactions (annotation relevant) and previously known interactions adds additional complexity to these tasks.
The histone deacetylase inhibitor, CBHA, inhibits growth of human neuroblastoma xenografts in vivo, alone and synergistically with all-trans retinoic acid. (2001)

Histone deacetylase inhibitors (HDACIs) inhibit the growth of a variety of transformed cells in culture. We demonstrated previously that the hybrid-polar HDACI m-carboxycinnamic acid bis-hydroxamide (CBHA) induces apoptosis of human neuroblastoma in vitro and is effective in lower doses when combined with retinoids. The current study investigates the effect of CBHA on the growth of human neuroblastoma in vivo, both alone and in combination with all-trans retinoic acid (atRA), using a severe combined immunodeficiency-mouse xenograft model. CBHA (50, 100, and 200 mg/kg/day) inhibited growth of SMS-KCN-69n tumor xenografts in a dose-dependent fashion, with 200 mg/kg CBHA resulting in a complete suppression of tumor growth. The efficacy of 50 and 100 mg/kg CBHA was enhanced by the addition of 2.5 mg/kg atRA. This dose of atRA was ineffective when administered alone. Treatment was accompanied by mild weight loss in all groups except the lowest dose of CBHA. Our results suggest HDACIs alone or combined with retinoids may have therapeutic utility for neuroblastoma.
Frequent Mutation of BAP1 in Metastasizing Uveal Melanomas (2010)

Metastasis is a defining feature of malignant tumors and is the most common cause of cancer-related death, yet the genetics of metastasis are poorly understood. We used exome capture coupled with massively parallel sequencing to search for metastasis-related mutations in highly metastatic uveal melanomas of the eye. Inactivating somatic mutations were identified in the gene encoding BRCA1-associated protein 1 (BAP1) on chromosome 3p21.1 in 26 of 31 (84%) metastasizing tumors, including 15 mutations causing premature protein termination and 5 affecting its ubiquitin carboxyl-terminal hydrolase domain. One tumor harbored a frameshift mutation that was germline in origin, thus representing a susceptibility allele. These findings implicate loss of BAP1 in uveal melanoma metastasis and suggest that the BAP1 pathway may be a valuable therapeutic target.
Two Genetic Loci Produce Distinct Carbohydrate-Rich Structural Components of thePseudomonas aeruginosaBiofilm Matrix (2004)

Pseudomonas aeruginosa forms biofilms, which are cellular aggregates encased in an extracellular matrix. Molecular genetics studies of three common autoaggregative phenotypes, namely wrinkled colonies, pellicles, and solid-surface-associated biofilms, led to the identification of two loci, pel and psl, that are involved in the production of carbohydrate-rich components of the biofilm matrix. The pel gene cluster is involved in the production of a glucose-rich matrix material in P. aeruginosa strain PA14 (L. Friedman and R. Kolter, Mol. Microbiol. 51:675-690, 2004). Here we investigate the role of the pel gene cluster in P. aeruginosa strain ZK2870 and identify a second genetic locus, termed psl, involved in the production of a mannose-rich matrix material. The 11 predicted protein products of the psl genes are homologous to proteins involved in carbohydrate processing. P. aeruginosa is thus able to produce two distinct carbohydrate-rich matrix materials. Either carbohydrate-rich matrix component appears to be sufficient for mature biofilm formation, and at least one of them is required for mature biofilm formation in P. aeruginosa strains PA14 and ZK2870.
CLASSIFICATION/CATEGORIZATION MODEL OF INSTRUCTION FOR LEARNING DISABLED STUDENTS (1987)

ABSTRACT A suitable correlation can be made to represent the simulated distillation of heavy oils starting from thennoaravimetric measurements. This method is applicable to hydrocarbons having an initial boiling point equal or greater than 200°C. The simulated thermogravimetric distillation fit was obtained from experiments with the standard compounds obtained from ASTM D-2887-83 (Boiling range distribution of petroleum fractions by gas chromatography). This method is simple, fast and without problems when applied to heavy feedstocks The data were used in the determination of average boiling temperatures of products from thermal cracking and thermal hydrocracking. It was also possible to quantify coke yields Average relative molecular masses of products from the above processes correlated well with the average boiling point temperatures. It indicates that, with respect to the hydrocarbon types, thermal cracking is not selective in comparison with thermal hydrocracking The equation applied to find the average boiling temperature is following: T = (1/al) (Ttg-a2). T is the boiling temperature, al and a2 are the correction factors, Ttg is the thermogravimetric temperature.
The left atrial appendage: our most lethal human attachment! Surgical implications✩ (2000)

The left atrial appendage is a lethal source of emboli in atrial fibrillation patients. As patients age and often develop atrial fibrillation, prophylactic appendage removal whenever the chest is open is suggested as a method to prevent future strokes. In chronic atrial fibrillation patients, appendectomy can be done with a mini-thorascopic approach. Further studies are planned to demonstrate the effectiveness of appendectomy in preventing strokes in the chronic fibrillating patients.
Identification of endoglin as a functional marker that defines long-term repopulating hematopoietic stem cells (2002)

We describe a strategy to obtain highly enriched long-term repopulating (LTR) hematopoietic stem cells (HSCs) from bone marrow side-population (SP) cells by using a transgenic reporter gene driven by a stem cell enhancer. To analyze the gene-expression profile of the rare HSC population, we developed an amplification protocol termed "constant-ratio PCR," in which sample and control cDNAs are amplified in the same PCR. This protocol allowed us to identify genes differentially expressed in the enriched LTR-HSC population by oligonucleotide microarray analysis using as little as 1 ng of total RNA. Endoglin, an ancillary transforming growth factor beta receptor, was differentially expressed by the enriched HSCs. Importantly, endoglin-positive cells, which account for 20% of total SP cells, contain all the LTR-HSC activity within bone marrow SP. Our results demonstrate that endoglin, which plays important roles in angiogenesis and hematopoiesis, is a functional marker that defines LTR HSCs. Our overall strategy may be applicable for the identification of markers for other tissue-specific stem cells.
A Mammalian Scaffold Complex That Selectively Mediates MAP Kinase Activation (1998)

The c-Jun NH2-terminal kinase (JNK) group of mitogen-activated protein (MAP) kinases is activated by the exposure of cells to multiple forms of stress. A putative scaffold protein was identified that interacts with multiple components of the JNK signaling pathway, including the mixed-lineage group of MAP kinase kinase kinases (MLK), the MAP kinase kinase MKK7, and the MAP kinase JNK. This scaffold protein selectively enhanced JNK activation by the MLK signaling pathway. These data establish that a mammalian scaffold protein can mediate activation of a MAP kinase signaling pathway.
Radiation Dose-Rate: A Factor of Importance in Radiobiology and Radiotherapy (1972)

A wide range of dose-rates has been used in radiobiology or radiotherapy, extending from a few rads per day to thousands of rads in a fraction of a second. At ultra-high dose-rates (pulses of micro or nanoseconds) a clear dose-rate effect has been demonstrated for bacteria, but is less certain for mammalian cells; these doserates have no certain application in radiotherapy at the present time. The principal dose-rate effect is observed between 100 rads/minute and 10 rads/hour; the cell-killing effect of X or γ rays decreases continuously as the dose-rate decreases throughout this range, and may be explained readily in terms of the repair of sub-lethal damage taking place during the irradiation. At lower dose-rates cell proliferation continues during the irradiation, and the ultimate outcome is a complex function of cellular radiosensitivity, dose/cell cycle and tissue adaptability. In clinical radiotherapy, the traditional pattern of high dose-rate for external beam therapy and low dose-rate for intracavitary and interstitial therapy has been challenged in recent years. The Cathetron has made possible the use of a high dose-rate fractionated regime for intracavitary treatment of carcinoma of the cervix and for surface mould applications. Conversely, beam therapy at low dose-rate (100 rads/hour) has been proposed and introduced recently, in an attempt to combine the, allegedly, superior results of radium with the safety and convenience of a beam therapy set-up.
Heat Shock Response (2022)

INTRODUCTION: HISTORICAL ROOTS. STRESS PROTEINS and GENES. Inducers: Heat Shock and Chemical Stressors. Heat Shock Proteins. HSP-Coding Genes. The Glucose-Regulated Proteins (GRP). RNAs as Heat Shock Products. Gene Technology and Functional Analyses of hs Genes. The Heat Shock Transcription Factor. Control of HSP Synthesis. PROGRAMMING of CELLULAR ACTIVITIES. Chromatin Structure, Transcription and Pre-mRNP Processing. Synthesis and Degradation of Ribosomes. Translational Control. Modification and Degradation of Proteins. Recovery of Gene Expression. Heat Shock-Induced Changes of Cell Ultrastructure. Cell Cycle and DNA Synthesis. Intracellular Localization of Heat Shock Proteins. Induced Thermotolerance. Heat Shock Induced Developmental Effects. Hyperthermia and Virus Multiplication. Hyperthermic Treatment of Cancer.
Conformationally defined adrenergic agents. 4. 1-(Aminomethyl)phthalans: synthesis and pharmacological consequences of the phthalan ring oxygen atom (1987)

The synthesis of a series of 1-(aminomethyl)phthalans 1b is reported. The radioligand binding to alpha 1- and alpha 2-receptors and the in vitro pharmacology in alpha 1 (rabbit aorta) and alpha 2 (phenoxybenzamine-pretreated dog saphenous vein) tissues were determined and were compared to the activity of the corresponding 1-(aminomethyl)indans. The activity of this series of phthalans was found to be consistent with the electrostatic repulsion hypothesis that was used to design the parent indan (ERBCOP) compounds. The effect of the phthalan ring oxygenation was to somewhat improve alpha 1-receptor potency relative to the 6-ERBCOP indans without having a general effect on the alpha 2-receptor potency. We conclude from the overall pattern of activity that while the norepinephrine type beta-hydroxyl group may be beneficial for binding to the alpha 1-adrenoceptor, it is not required for strong binding to or full stimulation of the alpha 2-adrenergic receptor, provided that the conformational mobility associated with the phenylethylamine is restricted and maintained in a favorable conformation for receptor interaction.
Radar Speed Monitoring System (2002)

Describes the Radar Speed Monitoring System which has been developed to create safe and comfortable traffic conditions. The system checks the velocity of vehicles and the photographs of speeding cars are centralized to an optical disk in a traffic control center. The system is helpful in managing speeding car enforcement.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>
Characterization of a morphological checkpoint coupling cell‐specific transcription to septation in Bacillus subtilis (1999)

Early in the process of spore formation in Bacillus subtilis, asymmetric cell division produces a large mother cell and a much smaller prespore. Differentiation of the prespore is initiated by activation of an RNA polymerase sigma factor, sigmaF, specifically in that cell. sigmaF is controlled by a regulatory cascade involving an anti-sigma factor, SpoIIAB, an anti-anti-sigma factor, SpoIIAA, and a membrane-bound phosphatase, SpoIIE, which converts the inactive, phosphorylated form of SpoIIAA back to the active form. SpoIIE is required for proper asymmetric division and much of the protein is sequestered into the prespore during septation. Importantly, activation of sigmaF is dependent on formation of the asymmetric septum. We have now characterized this morphological checkpoint in detail, using strains affected in cell division and/or spoIIE function. Surprisingly, we found that significant dephosphorylation of SpoIIAA occurred even in the absence of septation. This shows that the SpoIIE phosphatase is at least partially active independent of the morphological event and also that cells can tolerate significant levels of unphosphorylated SpoIIAA without activating sigmaF. We also describe a spoIIE mutant in which the checkpoint is bypassed, probably by an increase in the dephosphorylation of SpoIIAA. Taken together, the results support the idea that sequestration of SpoIIE protein into the prespore plays an important role in the control of sigmaF activation and in coupling this activation to septation.
Direct Photoaffinity Labeling of Tubulin With Taxol (1992)

This observation is the first step in a study to determine the binding site for taxol on the microtubule.
The Value of Acute-Phase Protein Measurements After Curative Gastric Cancer Surgery (1999)

An acute-phase protein response may be a predictive factor in the early stages of tumor recurrence. Acute-phase protein measurement provided clinically useful information about tumor recurrence after curative gastric cancer surgery.