gebhart/patrepeval huggingface dataset:
Requirements for clustering data streams (2002)

Scientific and industrial examples of data streams abound in astronomy, telecommunication operations, banking and stock-market applications, e-commerce and other fields. A challenge imposed by continuously arriving data streams is to analyze them and to modify the models that explain them as new data arrives. In this paper, we analyze the requirements needed for clustering data streams. We review some of the latest algorithms in the literature and assess if they meet these requirements.
Aspects of Incompressibility (1989)

The nuclear matter incompressibility K{sub {infinity}} (usually called the compressibility'' for some reason lost in antiquity) has been receiving an increasing amount of attention lately. Quite a spirited discussion is underway between groups who favor rather low values for use in simulations of supernova explosions, those who favor much higher values for the explanation of certain measurements in high-energy nuclear collisions, and many others who favor various intermediate values. The purpose of this paper is to present some preliminary results concerning the value of K{sub {infinity}} arising from a statistical model of macroscopic nuclear properties that is currently under development by Wladek Swiatecki and myself. This model, which is described in the next section, is meant to serve as a replacement for the traditional Liquid Drop Model and Droplet Model and their various extensions. It is itself an extension of the Thomas-Fermi approach of Seyler and Blanchard. However, it is important to note that we do not regard this approach as a poor approximation to Hartree-Fock, but rather as a vast improvement over the traditional LDM type approaches with their obvious limitations for light nuclei, at the drip lines, for large deformations, and other extreme situations such as large amounts of angular momentum or electric charge. 11 refs., 4 figs.
The fifth gene of the iol operon of Bacillus subtilis, iolE, encodes 2-keto-myo-inositol dehydratase (2004)

The myo-inositol catabolism pathway of Bacillus subtilis has not been fully characterized but was proposed to involve step-wise multiple reactions that finally yielded acetyl-CoA and dihydroxyacetone phosphate. It is known that the iolABCDEFGHIJ operon is responsible for the catabolism of inositol. IolG catalyses the first step of myo-inositol catabolism, the dehydrogenation of myo-inositol, producing 2-keto-myo-inositol (inosose). The second step was thought to be the dehydration of inosose. Genetic and biochemical analyses of the iol genes led to the identification of iolE, encoding the enzyme for the second step of inositol catabolism, inosose dehydratase. The reaction product of inosose dehydratase was identified as D-2,3-diketo-4-deoxy-epi-inositol.
Reprogramming somatic cells into stem cells (2006)

Recent scientific achievements in cell and developmental biology have provided unprecedented opportunities for advances in biomedical research. The demonstration that fully differentiated cells can reverse their gene expression profile to that of a pluripotent cell, and the successful derivation and culture of human embryonic stem cells (ESCs) have fuelled hopes for applications in regenerative medicine. These advances have been put to public scrutiny raising legal, moral and ethical issues which have resulted in different levels of acceptance. Ethical issues concerning the use of cloned human embryos for the derivation of stem cells have stimulated the search for alternative methods for reversing differentiated cells into multi/pluripotent cells. In this article, we will review the present state of these reprogramming technologies and discuss their relative success. We also overview reprogramming events after somatic cell nuclear transfer (SCNT), as they may further instruct ex ovo strategies for cellular manipulation.
A malignant pleural effusion infected with Salmonella enteritidis. (1996)

A patient is described with a unilateral pleural effusion persistently infected with Salmonella enteritidis. The infection was eventually eradicated with ciprofloxacin. A computed tomographic scan and mediastinal lymph node biopsy demonstrated an underlying small cell bronchogenic carcinoma.
Amino Acid-Derived Iodobenzene Dicarboxylates:  Reagents for Oxidative Conversion of Alkenes to Amino Acid Esters (2004)

[reaction: see text] New amino acid-derived iodobenzene dicarboxylates were prepared by the reaction of (diacetoxyiodo)benzene with N-protected natural amino acids. These compounds in the presence of iodide anion can be used as reagents for beta-iodocarboxylation of alkenes leading to the respective amino acid esters.
Bacteriophage T4 nrdA and nrdB genes, encoding ribonucleotide reductase, are expressed both separately and coordinately: characterization of the nrdB promoter (1990)

We examined the expression of the bacteriophage T4 nrdA and nrdB genes, which encode the alpha 2 and beta 2 subunits, respectively, of ribonucleoside diphosphate reductase, the first committed enzyme in the pathway of synthesis of the deoxyribonucleoside triphosphates. T4 nrdA, located 700 bp upstream from nrdB, has been shown previously to be transcribed by two major transcripts: a prereplicative, polycistronic message, TU, orginating at an immediate-early promoter, PE, that is 3.5 kb upstream from nrdA, and a postreplicative message commencing from a late promoter in its 5' flank. We have found a third promoter initiating a transcript at 159 nucleotides upstream from the reading frame of nrdB. PnrdB functions only in the presence of the T4 motA gene product, which is required for middle (time) promoters, and therefore the onset of nrdB transcription is delayed more than 2 min after infection. Because of the distance of nrdA from PE, the inception of nrdA transcription (delayed early) coincides closely with that of nrdB. An apparent termination site, tA, occurs about 80 bp downstream from nrdA. Some of the polycistronic mRNA reading through the site after 5 min contributes to nrdB transcription. nrdA and nrdB genes in an uninfected host have been reported to be transcribed only coordinately. In contrast, T4 nrdA and nrdB are initially transcribed separately onto the PE and PnrdB transcripts, respectively, but at about 5 min after infection are transcribed both coordinately and on separate transcripts. Evidence is presented that TU coordinately transcribes a deoxyribonucleotide operon in the order: frd, td, gene 'Y,' nrdA, nrdB. Since the beta 2 subunit is known to be formed after the alpha 2 subunit, the expression of the nrdB gene determines the onset of deoxyribonucleoside triphosphate synthesis and thus of T4 DNA replication.
Impairment of NO-Dependent Relaxation in Intralobar Pulmonary Arteries: Comparison of Urban Particulate Matter and Manufactured Nanoparticles (2008)

In contrast to manufactured particles (including nanoparticles), urban PM impairs NO but not cGMP responsiveness in intrapulmonary arteries. We attribute this effect to oxidative-stress-independent inflammatory response, resulting in decreased guanylyl cyclase activation by NO. Such impairment of the NO pathway may contribute to urban-PM-induced cardiovascular dysfunction.
Molecular Basis for ADP-induced Platelet Activation (1998)

ADP is an important platelet agonist causing shape change from smooth discoid shape to spiculated spheres and platelet aggregation. However, the molecular mechanisms involved in ADP-induced platelet activation have not been elucidated. We demonstrated earlier the existence of two distinct ADP receptors on platelets, one coupled to phospholipase C, P2TPLC, and the other to inhibition of adenylyl cyclase, P2TAC (Daniel, J. L., Dangelmaier, C., Jin, J., Ashby, B., Smith, J. B., and Kunapuli, S. P. (1998) J. Biol. Chem. 273, 2024-2029), in addition to the previously described P2X1 receptor. Here we report the cloning of a cDNA clone encoding the P2Y1 receptor from a human platelet cDNA library by homology screening with radiolabeled P2Y1-P2Y6 receptor cDNAs. ADP or 2-methyl(thio)-ADP-induced intracellular calcium increases were inhibited by the P2Y1 receptor-specific antagonists, adenosine 3'-phosphate 5'-phosphosulfate (A3P5PS), adenosine 3'-phosphate 5'-phosphate (A3P5P), and adenosine 2'-phosphate 5'-phosphate (A2P5P), in a concentration-dependent manner, but not by ARL 66096 or alpha, beta-MeATP. A3P5PS, A3P5P, and A2P5P also inhibited the shape change of aspirinated platelets induced by 10 microM ADP or 3 microM 2-methyl-(thio)-ADP in a concentration-dependent manner, with complete inhibition occurring at 300 microM. On the other hand ARL 66096 (100 nM), a potent P2TAC antagonist and alpha, beta-methylene-ATP (40 microM), a P2X1 receptor agonist, had no effect on ADP-induced platelet shape change. On the contrary, ADP-induced inhibition of adenylyl cyclase was blocked by ARL 66096, but not by alpha, beta-MeATP or the P2Y1 receptor-specific antagonists, A3P5PS, A3P5P, or A2P5P. These results demonstrate the role of the P2Y1 receptor in ADP-induced platelet shape change and calcium mobilization and support the idea that several P2 receptors are involved in the regulation of different aspects of platelet stimulus-response coupling.
Renal Sympathetic Denervation for Treatment of Drug-Resistant Hypertension (2012)

Control patients who crossed over to renal denervation with the Symplicity system had a significant drop in blood pressure similar to that observed in patients receiving immediate denervation. Renal denervation provides safe and sustained reduction of blood pressure to 1 year.
NMR Studies of Model Peptides of PHGGGWGQ Repeats within the N-Terminus of Prion Proteins: A Loop Conformation with Histidine and Tryptophan in Close Proximity (2000)

The N-terminal region of the prion protein from human and mouse contains five tandem repeats with the consensus sequence of PHGGGWGQ. NMR studies were performed in water for two cyclic peptides, cyclo-[C(1)R(2)Q(3)P(4)H(5)G(6)G(7)S(8)W(9)G(10)Q(11)R(12)D(13)C(14)] (C1) and cyclo-[C(1)R(2)D(3)P(4)H(5)G(6)G(7)G(8)W(9)G(10)Q(11)P(12)H(13)G(14)G (15)G(16)W(17)G(18)Q(19)R(20)D(21)C(22)] (C2), which are cyclized by a disulfide bridge between the Cys residues at the N- and C-termini, and for their corresponding linear peptides (L1 and L2) which are formed by reduction. The patterns of the C(alpha)H chemical shift difference of these four peptide mimetics were very similar to those observed for the tandem repeats of human prion protein reported by other researchers. The medium-range NOE connectivities were found between the C(beta)H of the H5 and the proton of the W9 side chain for L1. The corresponding NOEs were also observed in H5-W9 and H13-W17 of L2 with ambiguity. These observations indicate that histidine (i) is in close proximity to tryptophan (i+4). d(alphaN) (i,i+2) NOE connectivities were observed between W9 and Q11 of L1 and L2, and d(NN) (i,i+1) NOE connectivities were also observed for G10-Q11 of L1 and L2 and for G18-Q19 of L2. Significantly lower temperature coefficients of amide proton chemical shifts were obtained for Q11 and Q19 of L2 and C2. Structure calculations for L1 showed that HGG(G/S)W and (G/S)WGQ adopt a loop conformation and a beta-turn, respectively. These results strongly suggest that the tandem repeats within prion protein adopt a non-random structure.
Enhancement of the Second Harmonic Response by Adsorbates on Gold Colloids: The Effect of Aggregation (1999)

The extinction profiles as well as the hyper Rayleigh scattering signal of a highly monodisperse 22 nm diameter gold colloidal sol in the presence of pyridine have been measured. A strong enhancement of the HRS signal is observed in the presence of small amounts of pyridine. The relationship between the extinction spectra, the distribution of aggregated particles, and the second harmonic response has been investigated by evaluating the enhancement factor of the electromagnetic field in the colloids as they slowly aggregate. It is also shown that at larger pyridine concentrations, the hyper Rayleigh scattering signal levels off owing to the formation of large aggregates.
Runx1 stabilizes the mammary epithelial cell phenotype and prevents epithelial to mesenchymal transition (2017)

Runx1 is a well characterized transcription factor essential for hematopoietic differentiation and Runx1 mutations are the cause of leukemias. Runx1 is highly expressed in normal epithelium of most glands and recently has been associated with solid tumors. Notably, the function of Runx1 in the mammary gland and how it is involved in initiation and progression of breast cancer is still unclear. Here we demonstrate the consequences of Runx1 loss in normal mammary epithelial and breast cancer cells. We first observed that Runx1 is decreased in tumorigenic and metastatic breast cancer cells. We also observed loss of Runx1 expression upon induction of epithelial-mesenchymal transition (EMT) in MCF10A (normal-like) cells. Furthermore depletion of Runx1 in MCF10A cells resulted in striking changes in cell shape, leading to mesenchymal cell morphology. The epithelial phenotype could be restored in breast cancer cells by re-expressing Runx1. Analyses of breast tumors and patient data revealed that low Runx1 expression is associated with poor prognosis and decreased survival. We addressed mechanisms for the function of Runx1 in maintaining the epithelial phenotype and find Runx1 directly regulates E-cadherin; and serves as a downstream transcription factor mediating TGFβ signaling. We also observed through global gene expression profiling of growth factor depleted cells that induction of EMT and loss of Runx1 is associated with activation of TGFβ and WNT pathways. Thus these findings have identified a novel function for Runx1 in sustaining normal epithelial morphology and preventing EMT and suggest Runx1 levels could be a prognostic indicator of tumor progression.
Small Molecule Inhibitor of Mitotic Spindle Bipolarity Identified in a Phenotype-Based Screen (1999)

Small molecules that perturb specific protein functions are valuable tools for dissecting complex processes in mammalian cells. A combination of two phenotype-based screens, one based on a specific posttranslational modification, the other visualizing microtubules and chromatin, was used to identify compounds that affect mitosis. One compound, here named monastrol, arrested mammalian cells in mitosis with monopolar spindles. In vitro, monastrol specifically inhibited the motility of the mitotic kinesin Eg5, a motor protein required for spindle bipolarity. All previously known small molecules that specifically affect the mitotic machinery target tubulin. Monastrol will therefore be a particularly useful tool for studying mitotic mechanisms.
Laforin, a protein with many faces: glucan phosphatase, adapter protein, et alii (2012)

Lafora disease (LD) is a rare, fatal neurodegenerative disorder characterized by the accumulation of glycogen-like inclusions in the cytoplasm of cells from most tissues of affected patients. One hundred years after the first description of these inclusions, the molecular bases underlying the processes involved in LD physiopathology are finally being elucidated. The main cause of the disease is related to the activity of two proteins, the dual-specificity phosphatase laforin and the E3-ubiquitin ligase malin, which form a functional complex. Laforin is unique in humans, as it is composed of a carbohydrate-binding module attached to a cysteine-based catalytic dual-specificity phosphatase domain. Laforin directly dephosphorylates glycogen, but other proteinaceous substrates, if they exist, have remained elusive. Recently, an emerging set of laforin-binding partners apart from malin have been described, suggestive of laforin roles unrelated to its catalytic activity. Further investigations based on different transgenic mouse models have shown that the laforin-malin complex is also involved in other cellular processes, such as response to endoplasmic reticulum stress and misfolded protein clearance by the lysosomal pathway. However, controversial data and some missing links still make it difficult to assess the concrete relationship between glycogen deregulation and neuronal damage leading to the fatal symptoms observed in LD patients, such as myoclonic seizures and epilepsy. Consequently, clinical treatments are far from being achieved. In the present review, we focus on the knowledge of laforin biology, not only as a glucan phosphatase, but also as an adaptor protein involved in several physiological pathways.
Is the survival of melanoma patients receiving polyvalent melanoma cell vaccine linked to the human leukocyte antigen phenotype of patients? (1998)

The studies indicate that overall survival following PMCV treatment in melanoma patients significantly correlates with their HLA phenotypes. These correlations may be related to the host immune response to the PMCV or due to differences in the clinical course of melanoma in patients with different HLA types.
A direct antenna modulation (DAM) transmitter with a switched electrically small antenna (2010)

The first demonstration of a DAM transmitter with an electrically small antenna is presented in this paper. Traditionally efficiency-bandwidth product of an electrically small radiation system is inversely proportional to radiation Q of the antenna, which is high in nature according to radiation wave properties. However, a DAM transmitter operates in time-variant mode so that its efficiency-bandwidth product is not limited by Q. The key to improve the efficiency-bandwidth product is to decouple far-field radiation energy from near-field reactive energy. In DAM scheme, far field radiation is directly turned on and off to represent information, while a maximum reactive energy is circulated within system to enhance efficiency-bandwidth performance. To prove the concept, a traditional and a DAM transmitter have been tested and compared under the same condition. Results show that information tone received from the DAM transmitter is significantly higher in magnitude when signal bandwidth exceeds bandwidth of the traditional transmitter.
Better Subset Regression Using the Nonnegative Garrote (1995)

Abstract A new method, called the nonnegative (nn) garrote, is proposed for doing subset regression. It both shrinks and zeroes coefficients. In tests on real and simulated data, it produces lower prediction error than ordinary subset selection. It is also compared to ridge regression. If the regression equations generated by a procedure do not change drastically with small changes in the data, the procedure is called stable. Subset selection is unstable, ridge is very stable, and the nn-garrote is intermediate. Simulation results illustrate the effects of instability on prediction error. KEY WORDS: Little bootstrapModel errorPredictionStability
NCAM (CD56)-Positive Malignant Lymphoma (1993)

CD56 has been found to identify an isoform of the neural cell adhesion (NCAM). NCAM is a member of the immunoglobulin superfamily of cell adhesion molecules; it is related to a variety of leukocyte antigens and to several cell adhesion molecules believed relevant to malignant behavior in a variety of neoplasms. It contains polysialic acid, which appears to regulate binding avidity of NCAM and other cell adhesion processes. We have identified a group of NCAM-positive lymphomas. Compared to a group of NCAM-negative lymphomas, this group exhibited frequent involvement of unusual sites and a generally aggressive course. Another series of CD56-positive hematolymphoid malignancies has recently been described, from Hong Kong; this group also exhibited involvement of unusual sites and displayed a very aggressive course. Together these series suggest that NCAM on lymphoma is of biological and clinical significance in terms of tumor behavior and spread.
Growth Inhibition With Reversible Cell Cycle Arrest of Carcinoma Cells by Flavone L86-8275 (1992)

These findings suggest that L86-8275 is a candidate for further preclinical development, as well as a model for the synthesis of other flavonoids that might potently delay cell cycle progression to achieve inhibition of tumor growth. Future studies need to address optimal schedules for antiproliferative activity in vivo and inhibition of clonogenic activity.
Protein blotting : a practical approach (1994)

1. Historical Introduction SECTION 1: BASIC EQUIPMENT AND METHODS FOR PROTEIN BLOTTING 2. Introdcution and basic set-up for protein transfer 3. Protein blotting and immunoblotting using nitrocellulose membranes 4. Protein blotting using polyvinylidene fluoride membranes 5. Protein blotting using semi-dry electrophoretic transfer equipment SECTION 2: PRINCIPLES AND METHODS FOR PREPARING SAMPLES FOR PROTEIN TRASNFER 6. Transfer and blocking conditions in immunoblotting 7. Sample preparation for electrophoresis and transfer 8. Strategy for purification of organelles from parasites: protein blotting as one of the initial steps SECTION 3: DETECTION METHODS AND USES IN IMMUNOBLOTTING 9. Radiometric methods for detection in blots 10. Bioluminescence-enhanced detection systems in protein blotting 11. Chemiluminescent detection systems for protein blotting SECTION 4: APPLICATIONS OF PROTEIN BLOTTING 12. Detection and characterization of glycoprotein carbohydrate chains after electrophoretic separation 13. DNA binding of immobilized proteins 14. Use of peptide ligands for the detection of binding proteins by Western blotting 15. Use of blotted proteins as immunogens 16. Amino acid sequence analysis of blotted proteins 17. Renaturative catalytic blotting of enzyme proteins
Dimethylpyridin-4-ylamine-Catalysed Alcoholysis of 2-Amino-N,N,N-Trimethyl-9H-purine-6-ylammonium Chloride: An Effective Route to O6-Substituted Guanine Derivatives from Alcohols with Poor Nucleophilicity (2002)

Dimethylpyridin-4-ylamine (DMAP)-catalysed reactions of 2-amino-N,N,N-trimethyl-9H-purine-6-ylammonium chloride with fluoropyridine methoxides and various other alkoxides in DMSO at 60 °C gave the corresponding coupling products in moderate to good yields between 20-87%. Under these reaction conditions, fluorinated O6-substituted Guanine derivatives have been synthesized which could not be obtained via known analogous literature procedures. The respective yields of known O6-substituted guanine derivatives could be significantly improved by using this method. The efficient use of DMAP as an excellent nucleophilic catalyst in the syntheses of O6-substituted Guanine derivatives has thus been demonstrated.