gebhart/patrepeval huggingface dataset:
On the Role of Nitric Oxide in Hippocampal Long-Term Potentiation (2003)

Nitric oxide (NO) functions in several types of synaptic plasticity, including hippocampal long-term potentiation (LTP), in which it may serve as a retrograde messenger after postsynaptic NMDA receptor activation. In accordance with a prediction of this hypothesis, and with previous findings using guinea pig tissue, exogenous NO, when paired with a short tetanus (ST) to afferent fibers, generated a stable NMDA receptor-independent potentiation of rat CA1 hippocampal synaptic transmission that occluded LTP. Contrary to predictions, however, the pairing-induced potentiation was abolished in the presence of NO synthase inhibitors, indicating that endogenous NO is required for exogenous NO to facilitate LTP. Periodic application of NO while endogenous NO synthesis was blocked indicated that a tonic low level is necessary on both sides of the NO-ST pairing for the plasticity to occur. A similar dependence on tonic NO seems to extend to LTP, because application of an NO synthase inhibitor 5 min after tetanic stimulation blocked LTP as effectively as adding it beforehand. The posttetanus time window during which NO operated was restricted to <15 min. Inhibition of the guanylyl cyclase-coupled NO receptor indicated that the potentiation resulting from NO-ST pairing and the NO signal transduction pathway during early LTP are both through cGMP. We conclude that NO does not function simply as an acute signaling molecule in LTP induction but has an equally important role outside this phase. The results resonate with observations concerning the role of the hippocampal NO-cGMP pathway in certain types of learning behavior.
Induction of primary, antiviral cytotoxic, and proliferative responses with antigens administered via dendritic cells (1993)

Cytotoxic T lymphocytes (CTL) play an essential role in recovery from viral infections, but induction of CTL responses with nonreplicating antigens is difficult to achieve. Exogenous antigens, such as viral proteins and peptides, normally induce CD4+ T-cell responses unless appropriately delivered to the major histocompatibility complex class I antigen presentation pathway. In vitro studies performed to address this issue revealed a similar scenario, and primary CTL induction with nonreplicating antigens has rarely been reported. This study demonstrated primary antiviral CTL induction in vitro with exogenous antigens delivered in vivo to dendritic cells. This study also evaluated the efficacy of glycoprotein B peptide (free or encapsulated in liposomes), peptide-tripalmitoyl-S-glyceryl cysteinyl conjugate (acylpeptide), and glycoprotein B protein encapsulated in pH-sensitive liposomes as antigen delivery vehicles. Our results show that higher levels of cytotoxicity against herpes simplex virus type 1 resulted from exposure of dendritic cells to peptide-tripalmitoyl-S-glyceryl cysteinyl in liposomes. Macrophages treated in a similar manner were not effective stimulators for primary CTL induction. Our data have relevance to the understanding of mechanisms of antigen processing and presentation and the design of antiviral vaccines.
Propriedades reológicas de matérias-primas do Pólo Cerâmico de Santa Gertrudes provenientes da Formação Corumbataí (região de Rio Claro, SP) (2007)

Siltitos e argilitos da Formação Corumbataí são fontes de matéria-prima para a indústria cerâmica do Pólo de Santa Gertrudes. Litotipos provenientes de três minas (Tute, Granusso e Cruzeiro), localizadas na região de Rio Claro - SP, foram caracterizados quanto à curva de defloculação, conteúdo crítico de sólidos e tempo de envelhecimento (propriedades reológicas). Os litotipos representam desde a base até o topo da coluna estratigráfica dessa formação. Os resultados reológicos foram correlacionados com a composição mineralógica. Os representantes da base estratigráfica apresentaram boa defloculação, quase não necessitando adicionar defloculante, e, de forma geral, continham illita, feldspato, quartzo, hematita, clorita e interestraficados de clorita - argilomineral expansivo ou de illita - argilomineral expansivo. A maioria dos litotipos do topo defloculou, porém a quantidade ideal de defloculante foi superior aos adicionados às amostras da base. Os litotipos do topo continham carbonatos, além dos minerais supracitados. Uma amostra coletada no topo da mina Tute, com sinais evidentes de intemperismo, não defloculou. Os carbonatos presentes nos estratos superiores da formação e a alteração supérgena prejudicaram a defloculação. A quantidade máxima de sólidos na barbotina foi 66% em peso para os litotipos do topo da formação. Os litotipos testados apresentaram o fenômeno de envelhecimento da suspensão, porém as barbotinas, após 120 horas de seus preparos, ainda apresentavam viscosidades semelhantes àquelas usadas pela indústria de placas cerâmicas para revestimento.
Label-free spectroscopic detection of membrane potential using stimulated Raman scattering (2015)

Hyperspectral stimulated Raman scattering microscopy is deployed to measure single-membrane vibrational spectrum as a function of membrane potential. Using erythrocyte ghost as a model, quantitative correlation between transmembrane potential and Raman spectral profile was found. Specifically, the ratio between the area under Raman band at ∼2930 cm−1 and that at ∼2850 cm−1 increased by ∼2.6 times when the potential across the erythrocyte ghost membrane varied from +10 mV to −10 mV. Our results show the feasibility of employing stimulated Raman scattering microscopy to probe the membrane potential without labeling.
Cancer Evolution and the Limits of Predictability in Precision Cancer Medicine (2016)

The ability to predict the future behavior of an individual cancer is crucial for precision cancer medicine. The discovery of extensive intratumor heterogeneity and ongoing clonal adaptation in human tumors substantiated the notion of cancer as an evolutionary process. Random events are inherent in evolution and tumor spatial structures hinder the efficacy of selection, which is the only deterministic evolutionary force. This review outlines how the interaction of these stochastic and deterministic processes, which have been extensively studied in evolutionary biology, limits cancer predictability and develops evolutionary strategies to improve predictions. Understanding and advancing the cancer predictability horizon is crucial to improve precision medicine outcomes.
Patterns of change in cytochrome c oxidase redox status (2004)

Investigators using mono channel near infrared spectroscopy (NIRS) have reported different patterns of change in cytochrome c oxidase (Cyt) in similar studies of tissue ischaemia. We investigated whether there were distinctive differences in NIRS signals obtained simultaneously from different sampling sites during the same imposed physiological intervention within the same subject. Methods : Subjects were 36, healthy, 10 kg, commercial swine undergoing cardiopulmonary bypass to initiate 3 to 7 periods of 7.5 minutes of circulatory arrest. Each arrest was initiated at one of 81 combinations of high, normal, or low levels of core temperature, haematocrit, pH, and serum glucose. Each combination was repeated twice, yielding 162 NIRS data sets. Results : Six distinct patterns of change of Cyt were found. Typically, brain Cyt quickly became reduced shortly after the start of arrest, muscle Cyt did not start becoming reduced until after 3½ minutes of arrest, and spinal cord Cyt either did not change status or became gradually reduced throughout the period of arrest. The brain response may reflect strong oxygen dependence, while the muscle response may indicate a dependency buffered by myoglobin stores, and the spine response may indicate a low concentration of available Cyt that is too diffuse to be rapidly influenced by changes in oxygen availability. Conclusion : Multi‒channel NIRS is needed for systemic evaluation of respiration at the cellular level in clinical settings. Distinctive Cyt patterns of change occur in different organs at the same time, in response to circulatory arrest.
Rapid accumulation of Akt in mitochondria following phosphatidylinositol 3‐kinase activation (2003)

We describe here a new component of the phosphatidylinositol 3-kinase/Akt signaling pathway that directly impacts mitochondria. Akt (protein kinase B) was shown for the first time to be localized in mitochondria, where it was found to reside in the matrix and the inner and outer membranes, and the level of mitochondrial Akt was very dynamically regulated. Stimulation of a variety of cell types with insulin-like growth factor-1, insulin, or stress (induced by heat shock), induced translocation of Akt to the mitochondria within only several minutes of stimulation, causing increases of nearly eight- to 12-fold, and the mitochondrial Akt was in its phosphorylated, active state. Two mitochondrial proteins were identified to be phosphorylated following stimulation of mitochondrial Akt, the beta-subunit of ATP synthase and glycogen synthase kinase-3beta. The finding that mitochondrial glycogen synthase kinase-3beta was rapidly and substantially modified by Ser9 phosphorylation, which inhibits its activity, following translocation of Akt to the mitochondria is the first evidence for a regulatory mechanism affecting mitochondrial glycogen synthase kinase-3beta. These results demonstrate that signals emanating from plasma membrane receptors or generated by stress rapidly modulate Akt and glycogen synthase kinase-3beta in mitochondria.
AlgR3, a protein resembling eukaryotic histone H1, regulates alginate synthesis in Pseudomonas aeruginosa. (1990)

A regulatory mutation (alg52) in a Pseudomonas aeruginosa alginate-negative mutant (strain 8882) is complemented efficiently by the gene algR2 and somewhat inefficiently by a second gene termed algR3. algR3 and algR2 are located on a 4.4-kilobase-pair HindIII-BamHI fragment, which has been completely sequenced. algR2 has previously been characterized. Introduction of kanamycin-resistance cassettes and deletion-subcloning experiments involving various open reading frames in the HindIII-BamHI fragment have localized the algR3 gene, which encodes a 340-amino acid polypeptide. This highly basic regulatory protein contains 17% lysine and 36% alanine. The predicted amino acid sequence shows no significant similarity with any bacterial proteins and yet is highly similar to the sea urchin Lytechinus pictus histone H1 subtype of protein. Promoter localization by reverse transcriptase mapping of the algR3 gene shows the presence of Escherichia coli sigma 70 recognition sequences, and coupled transcription/translation experiments in E. coli demonstrate the presence of a 39-kDa polypeptide encoded by the cloned algR3 gene.
DFD based scene segmentation for H.263 video sequences (2003)

Content based indexing and retrieval of video is becoming increasingly important in many applications. Identifying scene changes and special effects in a video scene is an essential pre-requisite for indexing. In this paper, a sudden scene change detection algorithm for H.263 video sequences is proposed. This method uses the number of intra-coded macroblocks and displaced frame difference (DFD) signal of the video signal. Experimental results show that the performance of this algorithm is independent of the encoder threshold. Furthermore, this algorithm is capable of detecting abrupt scene changes accurately even if the video sequence contains special effects.
Use of bisphosphonates in the management of postmenopausal osteoporosis (2010)

Bisphosphonates are widely used in the treatment of postmenopausal osteoporosis. They decrease the rate of bone turnover, maintain or improve structural and material properties of bone, and increase bone mineral density and thereby decrease the risk of fractures. Available potent bisphosphonates can be given to patients by different dosing regimens that range from daily oral administration to yearly intravenous infusions. Controlled studies, extending to 10 years of continuous treatment, provide information about long-term efficacy and safety and can help in the planning of long-term treatment strategies. Selection of bisphosphonates for the treatment of individuals should be based on a careful review of efficacy data, a risk profile of the bisphosphonate, and values and preferences of the patient.
Association of Chlamydial Infection With Cerebrovascular Disease (1996)

We conclude that chronic infection with C pneumoniae is associated with an increased risk of stroke and transient ischemic events.
Template synthesis of nanoparticle arrays of gold, platinum and palladium in mesoporous silica films and powders (2004)

Mesoporous silica films were prepared on glass plates by a dip coating method, and the film/plate samples were used as a support for Au, Pt and Pd nanoparticles. By H2- or photo-reduction of metal precursors impregnated on the films, metal nanoparticles are formed with an ordered array structure in the mesopores. The nanoparticles are isolated by dissolving the silica film with a dilute HF solution, and the particles are stabilized with ligands such as 1-dodecanethiol and triphenylphosphine. The diameter of the separated nanoparticles is 2.5 nm with narrow distributions, showing that uniform particles are formed in the mesopores. Selective formation of metal nanoparticles rather than nanowires suggests that a 3D-hexagonal structure is involved in the 2D-hexagonal mesoporous silica films. To study the formation of nanoparticles in a 3D-hexagonal structure, HMM-2 powder was used as a support, and in fact Au and Pt nanoparticles are formed in the HMM-2 powders. The XRD study suggests that the Au nanoparticles in the film/plate have an anisotropic orientation in the mesoporous channels. The Au/film/plate sample gives a weak plasmon peak at 570–580 nm using diffuse-reflectance UV-visible spectroscopy, which is shifted to high wavelength by 50–60 nm compared with larger Au particles.
The bases of the nucleic acids of some bacterial and animal viruses: the occurrence of 5-hydroxymethylcytosine (1953)

After injection of 82p into young rats the specific activity of the free glycerylphosphorylethanolamine after short periods was always greater than that of the phosphatidylethanolamine. This suggests that glycerylphosphorylethanolamine is not an in vivo breakdown product of phosphatidylethanolamine, although other considerations indi- cate that it does not lie on the main synthetic pathway.
Three-dimensional visualization of protein expression in mouse brain structures using imaging mass spectrometry (2005)

We have developed a method to visualize matrix-assisted laser desorption ionization imaging mass spectrometry (MALDI IMS) data aligned with optically determinable tissue structures in three dimensions. Details of the methodology are exemplified using the 3-D reconstruction of myelin basic protein (MBP) in the corpus callosum of a mouse brain. In this procedure, optical images obtained from serial coronal sections are first aligned to each other to reconstruct a surface of the corpus callosum from segmented contours of the aligned images. The MALDI IMS data are then coregistered to the optical images and superimposed into the surface to create the final 3-D visualization. Correlating proteomic data with anatomical structures provides a more comprehensive understanding of healthy and pathological brain functions, and holds promise to be utilized in more complex anatomical arrangements.
Neural networks applied to pharmaceutical problems. V. Obtaining the correlation indices between drug activity and structural parameters using a neural network. (1991)

A linear operation was introduced to the neural network. We also studied a method that gives correlation coefficients between input parameters and outputs. It was difficult to obtain these coefficients. Instead, we proposed a new index, the divided difference of output intensity with respect to the input parameter (δO/δx). The divided differences were obtained using an unsaturated sigmoid function as an output function of neurons, where a new learning method with the concept of "neuron fatigue" is introduced. The new techniques were applied to quantitative structure-activity relationships (QSAR) studies in carboquinones and benzodiazepines to compare the results with those by multiregression analysis. It was found that the divided differences work well and can produce the equivalent partial differential coefficients that are obtained by multiregression analysis.
Recombinant EWS-FLI1 Oncoprotein Activates Transcription (2004)

The Ewing's sarcoma family of tumors (ESFT) contains a characteristic translocation the chimeric transcript of which is translated to become the EWS-FLI1 fusion protein. EWS-FLI1 regulates transcription and posttranscriptional splicing. Elimination of EWS-FLI1 protein from ESFT cells induces apoptosis and reduces xenograft tumor growth. Therefore the production of a biologically active recombinant EWS-FLI1 could lead to discoveries that would enhance our mechanistic understanding of ESFT. We have cloned, expressed, and purified a biologically active recombinant EWS-FLI1 in Escherichia coli using affinity column chromatography. A refolding procedure was required to render the recombinant EWS-FLI1 soluble in relatively native conditions. The structural alterations induced by the refolding procedure were monitored by SDS-gel electrophoresis, circular dichroism, and steady-state fluorescence spectroscopy. Recombinant EWS-FLI1 under native conditions approaches a largely unfolded conformation. Recombinant EWS-FLI1 protein under native conditions specifically binds to DNA and transcribes RNA. Our biologically active recombinant EWS-FLI1 oncoprotein will be useful to identify functional molecular partners and inhibitors.
Liver X Receptor Agonists Inhibit the Phospholipid Regulatory Gene CTP: Phosphoethanolamine Cytidylyltransferase-Pcyt2 (2008)

Metabolic pulse-chase experiments demonstrated that 25-hydroxycholesterol (25-OH), the endogenous activator of the liver X receptor (LXR), significantly reduced the biosynthesis of phosphatidylethanolamine via CDP-ethanolamine (Kennedy) pathway at the step catalyzed by CTP: phosphoethanolamine cytidylyltransferase (Pcyt2). In the mouse embryonic fibroblasts C3H10T1/2, the LXR synthetic agonist TO901317 lowered Pcyt2 promoter-luciferase activity in a concentration-dependent manner. Furthermore, 25-OH and TO901317 reduced mouse Pcyt2 mRNA and protein levels by 35-60%. The inhibitory effects of oxysterols and TO901317 on the Pcyt2 promoter function, mRNA and protein expression were conserved in the human breast cancer cells MCF-7. These studies identify the Pcyt2 gene as a novel target whereby LXR agonists may indirectly modulate inflammatory responses and atherosclerosis.
Thalidomide. A surprising recovery. (1997)

The epidemic of birth defects in Europe in the early 1960s attributed to thalidomide led to stringent and unprecedented drug safety requirements in many countries. No definitive mechanism of action has been determined for the biological activities associated with thalidomide. Food and Drug Administration and congressional concerns about the handling of clinical investigations of thalidomide led to sweeping new regulations for clinical trials. Thalidomide is currently being used clinically to treat such conditions as cachexia associated with HIV and cancer, mycobacterial disease, and autoimmune diseases.
Formation of Conjugated Δ8,Δ10-Double Bonds by Δ12-Oleic-acid Desaturase-related Enzymes (2001)

Divergent forms of the plant Delta(12)-oleic-acid desaturase (FAD2) have previously been shown to catalyze the formation of acetylenic bonds, epoxy groups, and conjugated Delta(11),Delta(13)-double bonds by modification of an existing Delta(12)-double bond in C(18) fatty acids. Here, we report a class of FAD2-related enzymes that modifies a Delta(9)-double bond to produce the conjugated trans-Delta(8),trans-Delta(10)-double bonds found in calendic acid (18:3Delta(8trans,10trans,12cis)), the major component of the seed oil of Calendula officinalis. Using an expressed sequence tag approach, cDNAs for two closely related FAD2-like enzymes, designated CoFADX-1 and CoFADX-2, were identified from a C. officinalis developing seed cDNA library. The deduced amino acid sequences of these polypeptides share 40-50% identity with those of other FAD2 and FAD2-related enzymes. Expression of either CoFADX-1 or CoFADX-2 in somatic soybean embryos resulted in the production of calendic acid. In embryos expressing CoFADX-2, calendic acid accumulated to as high as 22% (w/w) of the total fatty acids. In addition, expression of CoFADX-1 and CoFADX-2 in Saccharomyces cerevisiae was accompanied by calendic acid accumulation when induced cells were supplied exogenous linoleic acid (18:2Delta(9cis,12cis)). These results are thus consistent with a route of calendic acid synthesis involving modification of the Delta(9)-double bond of linoleic acid. Regiospecificity for Delta(9)-double bonds is unprecedented among FAD2-related enzymes and further expands the functional diversity found in this family of enzymes.
EU enlargement impacts – Theory and evidence (2007)

The past EU enlargements open different questions. Why EU has performed five enlargements in the past and why it is at present even envisaging future integration enlargements? The next question is “ How the theory and practical integration evidences could explain and support the past and future integration enlargementsl ; ? According to “ j-curve” logic each reform of the integration – including enlargements – could create, after its initial drop, a substantially higher GDP growth rate in comparison to long term growth rate possible when no change in the structure or functioning of economic integration happens. Dilemmas of such nature are intensified with the EU enlargements of 2004 and 2007. The paper show some possible ways of searching the answers to the above questions. In the first part it deals with development of the theoretical background of economic integration issues starting with the dilemmas about the theory of the second best solution. Paper shows that the theory and actual international trade environment have changed substantially after initial ideas of customs union creation in Europe. Changes are giving new possibilities of explaining the rational for economic integration efforts and as well new ways of presenting the integration effects on EU member countries. Following the idea of economic rational linked to EU integration and to its enlargement the paper presents and comments selected economic indicators related on integration effects specifics for Slovenia - recorded after the EU enlargement 2004.
Bacillus thuringiensis ssp. israelensis Cyt1Aa enhances activity of Cry11Aa toxin by facilitating the formation of a pre-pore oligomeric structure (2007)

Bacillus thuringiensis ssp. israelensis (Bti) has been used worldwide for the control of dipteran insect pests. This bacterium produces several Cry and Cyt toxins that individually show activity against mosquitoes but together show synergistic effect. Previous work demonstrated that Cyt1Aa synergizes the toxic activity of Cry11Aa by functioning as a membrane-bound receptor. In the case of Cry toxins active against lepidopteran insects, receptor interaction triggers the formation of a pre-pore oligomer that is responsible for pore formation and toxicity. In this work we report that binding of Cry11Aa to Cyt1Aa facilitates the formation of a Cry11Aa pre-pore oligomeric structure that is capable of forming pores in membrane vesicles. Cry11Aa and Cyt1A point mutants affected in binding and in synergism had a correlative effect on the formation of Cry11Aa pre-pore oligomer and on pore-formation activity of Cry11Aa. These data further support that Cyt1Aa interacts with Cry11Aa and demonstrate the molecular mechanism by which Cyt1Aa synergizes or suppresses resistance to Cry11Aa, by providing a binding site for Cry11Aa that will result in an efficient formation of Cry11Aa pre-pore that inserts into membranes and forms ionic pores.