gebhart/patrepeval huggingface dataset:
Studies of membrane heterogeneity using fluorescence associative techniques (1986)

Fluorescence spectra, decay times and emission anisotropy are capable of providing important information regarding the interaction of probes with biological macromolecules. Combinations of different fluorescence parameters can provide information about heterogeneity of liposomes or biological membranes and about the character of excited-state interactions of the fluorescence probe. Decay-associated spectra (DAS) or anisotropy decay associated spectra (ADAS) can be used to resolve heterogeneous species. These methods have been applied to the study of both pyrene and a pyrene methyl cholesterol adduct (PMC) with dimyristoyl-lecithin vesicles (DML). The data indicate microheterogeneity in the distribution of the probes above the phase transition. Anisotropy decay-associated spectra (ADAS) have been used to study diphenylhexatriene (DPH) in dipalmitoyl-lecithin (DPL) and dimyristoyl-lecithin (DML) vesicles. The results indicate that DPH inhabits more than one rotational environment in the liposome preparations used.
Experiments with Clifford Geometric Algebra Applied to Cryptography (2020)

The combination of flexibility, simplicity, elegance, and power that is found in Clifford Geometric Algebra (GA) is probably one of the main reasons for growing interest from those willing to explore new algebraic structures for producing many applications in physics, engineering, and computer science. As a result, to the surprise of many, existing applications, when modified to run as implementations of Clifford GA algorithms, demonstrate higher performance, better maintenance, less complexity, and a friendlier learning curve for those new to GA. Nevertheless, Clifford GA is virtually unexplored in cryptography, an area of science that can be greatly benefited by a mathematical tool equipped with the aforementioned potential. In this work, we introduce preliminary experiments of cryptographic solutions based on Clifford geometric algebra, including a key exchange protocol, a hash algorithm, and a private-key encryption scheme, with the hope of providing appealing pieces of evidence that this powerful mathematical resource is worth investigating as a strong candidate for broad adoption in cryptography. As proof of concept, we provide access to a library written in Ruby language in which we implement the ideas discussed in this work and where the reader will be able to find some predefined numerical examples.
Supplementary Table S3 from A Clinical PET Imaging Tracer ([<sup>18</sup>F]DASA-23) to Monitor Pyruvate Kinase M2–Induced Glycolytic Reprogramming in Glioblastoma (2023)

&lt;p&gt;Clinical Characteristics of patients imaged with [18F]DASA-23&lt;/p&gt;
Spatial mapping reveals granuloma diversity and histopathological superstructure in human tuberculosis (2023)

The hallmark of tuberculosis (TB) is the formation of immune cell-enriched aggregates called granulomas. While granulomas are pathologically diverse, their tissue-wide heterogeneity has not been spatially resolved at the single-cell level in human tissues. By spatially mapping individual immune cells in every lesion across entire tissue sections, we report that in addition to necrotizing granulomas, the human TB lung contains abundant non-necrotizing leukocyte aggregates surrounding areas of necrotizing tissue. These cellular lesions were more diverse in composition than necrotizing lesions and could be stratified into four general classes based on cellular composition and spatial distribution of B cells and macrophages. The cellular composition of non-necrotizing structures also correlates with their proximity to necrotizing lesions, indicating these are foci of distinct immune reactions adjacent to necrotizing granulomas. Together, we show that during TB, diseased lung tissue develops a histopathological superstructure comprising at least four different types of non-necrotizing cellular aggregates organized as satellites of necrotizing granulomas.
Neopikromycin and Novapikromycin from the Pikromycin Biosynthetic Pathway of Streptomyces venezuelae (2006)

Two new macrolides from the pikromycin biosynthetic pathway of Streptomyces venezuelae, neopikromycin (9) and novapikromycin (10), were identified and structurally characterized through mass spectrometry and NMR spectroscopy. The established structures showed that 9 and 10 have hydroxyl groups at C-14 (9) and at both C-12 and C-14 (10), on the basis of a comparison with narbomycin (7). The purified PikC cytochrome P450 monooxygenase catalyzes the in vitro hydroxylation of 7 and pikromycin (8) to yield 9 and 10, respectively, thus expanding the substrate- and regio-flexibility of this enzyme.
Cholestasis Is Associated with Hepatic Microvascular Dysfunction and Aberrant Energy Metabolism Before and During Ischemia-Reperfusion (2012)

Cholestatic livers possess sufficient antioxidative capacity to ameliorate radical-mediated damage during I/R. I/R-induced damage in cholestatic livers is predominantly caused by microvascular perfusion defects rather than exuberant oxidative/nitrosative stress. The forestalled rate of oxidative phophorylation and recovery of bioenergetic and possibly metabolic parameters during the early reperfusion phase are responsible for extensive liver damage.
Trans-acting elements modulate expression of the human c-myc gene in Burkitt lymphoma cells. (1986)

We have used a competition assay to identify the targets of trans-acting elements that modulate the expression of the human c-myc gene (designated MYC in human gene nomenclature). For this purpose, a c-myc hybrid indicator gene was formed by joining the c-myc promoter region, first noncoding exon, and intron to the bacterial gene for chloramphenicol acetyltransferase (CAT). The test assay consisted of cotransfecting the indicator gene with competing fragments of DNA derived from suspected control regions of the c-myc gene. Such experiments test the hypothesis that control regions are often targets for the binding of trans-acting regulatory factors that can be diverted to competing fragments of DNA. A negatively acting element will be diverted from the indicator gene, allowing the gene's enhanced expression, whereas a positively acting element will behave oppositely. Control indicator genes driven by non-myc promoters assess the specificity of the effect. Using this approach, we find three c-myc regions that are capable of enhancing the expression of the indicator gene in competition assays (i.e., putative sites of negative modulation). In addition, we find sequences near the c-myc promoters that suppress expression in competition assays (i.e., putative binding sites of positively acting factors). These results, with appropriate controls, suggest the existence of target sites near the c-myc gene that specifically modulate its expression both positively and negatively. Their locations fit well with regions damaged or lost in many Burkitt lymphoma and murine plasmacytoma translocations.
<title>NYNEX network exploratorium visualization tool: visualizing telephone network planning</title> (1996)

This paper describes a visualization tool which is a component of the NYNEX Network Exploratorium, a decision support platform for telephone interoffice network planning. The visualization tool provides a number of visualization styles suited to knowledge discovery in the network planning domain, and is designed for expansion to support additional styles. Visualizations are specific using a declarative language, which binds visual attributes directly to arbitrary attributes of objects in an object-oriented database. An overview of the language and some application examples are presented.
Automatic Processing Scheme for Low Laser Invasiveness Electro Optical Frequency Mapping mode (2016)

International audience
572. Antibiotic-Free Nonviral pFAR4 Vector Displays Efficient Transgene Delivery in Mouse and Human Cells (2015)

New generations of plasmid vectors used for non-viral gene therapy have a reduced size, thus allowing an increase in transfection efficiency and expression levels. We designed a novel vector, called pFAR4, which is Free of Antibiotic Resistance markers. In bacteria, the production of pFAR4 derivatives relies on a plasmid-borne function that suppresses a nonsense mutation introduced into an essential Escherichia coli gene. Thanks to its reduced size, pFAR4 appears to be an efficient gene vector as it displays a superior transgene expression level either after transfection of cultured B16 melanoma cells or electrotransfer into skin or tumors. Furthermore, hydrodynamic delivery into liver revealed that pFAR4 allowed a prolonged expression level, in comparison with kanamycin resistant plasmids that promote transgene silencing. We took advantage of the pFAR4 superiority in liver to assess a novel therapeutic approach for the Mucopolysaccharidosis type IIIA (MPS-IIIA) or Sanfilippo A syndrome. MPS-IIIA is a lysosomal storage genetic disease which results from the deficiency of the N-sulfoglucosamine sulfohydrolase (SGSH) protein, a sulfamidase required for the degradation of heparan sulfate glycosaminoglycans (GAGs). The accumulation of these macromolecules leads to somatic organ pathologies, severe neurodegeneration and patients’ death. In MPS-IIIA mice, hydrodynamic delivery of a pFAR4 derivative expressing the deficient enzyme from a liver-specific promoter allowed high and prolonged serum levels of sulfamidase protein that was efficiently taken-up by neighboring organs after its endocytosis by mannose 6-phosphate receptors-expressing cells. This led to the correction of GAG accumulation in all peripheral organs as well as in the brain, albeit at early stages of the disease. Improvement of our approach is provided by fusing the SGSH protein with peptides mediating transcytocis across the blood-brain barrier. Having established that pFAR4 is a potent expression vector in a non-integrative approach, our next step consisted in combining the pFAR4 technology and the Sleeping Beauty (SB) transposon system, which is composed of a transposase that excises the transgene-containing transposon from a donor plasmid and mediates its integration into the host cells’ genome. The reduced size of pFAR4 allowed an efficient delivery of SB components into human cells. Our current goal is to take the pFAR4 and Sleeping Beauty technologies to the clinic, in the context of an ex vivo gene therapy approach involving the transfection of autologous primary pigment epithelial cells for the treatment of neovascular age-related macular degeneration disease, in two phase I/II clinical trials.
Rare variants analysis of cutaneous malignant melanoma genes in Parkinson's disease (2016)

A shared genetic susceptibility between cutaneous malignant melanoma (CMM) and Parkinson's disease (PD) has been suggested. We investigated this by assessing the contribution of rare variants in genes involved in CMM to PD risk. We studied rare variation across 29 CMM risk genes using high-quality genotype data in 6875 PD cases and 6065 controls and sought to replicate findings using whole-exome sequencing data from a second independent cohort totaling 1255 PD cases and 473 controls. No statistically significant enrichment of rare variants across all genes, per gene, or for any individual variant was detected in either cohort. There were nonsignificant trends toward different carrier frequencies between PD cases and controls, under different inheritance models, in the following CMM risk genes: BAP1, DCC, ERBB4, KIT, MAPK2, MITF, PTEN, and TP53. The very rare TYR p.V275F variant, which is a pathogenic allele for recessive albinism, was more common in PD cases than controls in 3 independent cohorts. Tyrosinase, encoded by TYR, is the rate-limiting enzyme for the production of neuromelanin, and has a role in the production of dopamine. These results suggest a possible role for another gene in the dopamine-biosynthetic pathway in susceptibility to neurodegenerative Parkinsonism, but further studies in larger PD cohorts are needed to accurately determine the role of these genes/variants in disease pathogenesis.
Detergency (2016)

This Glossary of Terms Related to Pharmaceutics is needed by practitioners in the field of pharmaceutics as this field fulfills an important and crucial role, different from the roles of other scientific disciplines involved in the drugmaking process. The glossary contains 168 definitions used in pharmaceutics. These are related to various aspects of this discipline, such as: (1) physicochemical characterization of pharmaceutical preparations and the active ingredients they contain; (2) unit operations used in the practice of pharmaceutics; (3) terms related to the various dosage forms; (4) terms related to the various modes and routes of drug delivery; (5) terms used in pharmacokinetics and biopharmaceutics in general; and additional miscellaneous terms. The field of pharmaceutics itself is of a multidisciplinary nature as its practitioners come from a variety of disciplines, such as chemistry or various biological sciences, thus a glossary containing authoritative definitions would be useful for them. The terms used in pharmaceutics are rarely covered by existing glossaries, and in the cases they are, their definitions are often inappropriate for the field of pharmaceutics and require new or modified definitions to better fit the new context.
Identification of Novel Antigens Recognized by Serum Antibodies in Bovine Tuberculosis (2017)

Bovine tuberculosis (TB), caused by <i>Mycobacterium bovis</i>, remains an important zoonotic disease posing a serious threat to livestock and wildlife. The current TB tests relying on cell-mediated and humoral immune responses in cattle have performance limitations. To identify new serodiagnostic markers of bovine TB, we screened a panel of 101 recombinant proteins, including 10 polyepitope fusions, by a multiantigen print immunoassay (MAPIA) with well-characterized serum samples serially collected from cattle with experimental or naturally acquired <i>M. bovis</i> infection. A novel set of 12 seroreactive antigens was established. Evaluation of selected proteins in the dual-path platform (DPP) assay showed that the highest diagnostic accuracy (∼95%) was achieved with a cocktail of five best-performing antigens, thus demonstrating the potential for development of an improved and more practical serodiagnostic test for bovine TB.
Improved beta''-alumina electrolytes for advanced storage batteries. Final report (1983)

Investigations which seek to clarify the origin of electrolytic degradation of sodium-beta'' alumina solid electrolytes when used in sodium/sulfur cells are presented. Degradation is often observed on the sulfur as well as on the sodium side of the used electrolytes, although for some extensively used electrolytes no signs of any degradation could be detected. In most cases, large grains could be found to be associated with the initiation of Mode I failure, and controlled experiments showed that grain boundaries of such large grains were mechanically weak. Additionally, acoustic emission monitoring during current flow indicated that Mode I cracking could also progress by slow crack growth. This slow, subcritical crack growth is most important in the very early stages of growth of small cracks. Acoustic emission experiments on electrolytes toughened with a zirconia dispersion indicated that significant increases could be obtained in the threshold current densities at which Mode I degradation initiated.
Indicators for cognitive performance and subjective cognitive complaints in multiple sclerosis: a role for advanced MRI? (2013)

Previous studies showed that advanced neuroimaging measures (functional MRI, diffusion tensor imaging) could distinguish multiple sclerosis (MS) patients with and without cognitive impairment. Are these measures indeed better indicators for cognitive impairment or subjective cognitive complaints than conventional MRI? Fifty MS patients and 29 controls were investigated. Regression analysis, including socio-demographic data, disease characteristics, psychological measures, and (advanced) neuroimaging, showed that worse cognitive performance was associated with male sex, lower education, and lower gray matter volume. Subjective cognitive complaints were associated with fatigue and less hippocampal atrophy. Advanced MRI measures did not add to the predictive power of our model.
Towards Efficient I/O Scheduling for Collaborative Multi-Level Checkpointing (2021)

Efficient checkpointing of distributed data structures periodically at key moments during runtime is a recurring fundamental pattern in a large number of uses cases: fault tolerance based on checkpoint-restart, in-situ or post-analytics, reproducibility, adjoint computations, etc. In this context, multilevel checkpointing is a popular technique: distributed processes can write their shard of the data independently to fast local storage tiers, then flush asynchronously to a shared, slower tier of higher capacity. However, given the limited capacity of fast tiers (e.g. GPU memory) and the increasing checkpoint frequency, the processes often run out of space and need to fall back to blocking writes to the slow tiers. To mitigate this problem, compression is often applied in order to reduce the checkpoint sizes. Unfortunately, this reduction is not uniform: some processes will have spare capacity left on the fast tiers, while others still run out of space. In this paper, we study the problem of how to leverage this imbalance in order to reduce I/O overheads for multi-level checkpointing. To this end, we solve an optimization problem of how much data to send from each process that runs out of space to the processes that have spare capacity in order to minimize the amount of time spent blocking in I/O. We propose two algorithms: one based on a greedy approach and the other based on modified minimum cost flows. We evaluate our proposal using synthetic and real-life application traces. Our evaluation shows that both algorithms achieve significant improvements in checkpoint performance over traditional multilevel checkpointing.
Novel excitatoryConuspeptides define a new conotoxin superfamily (2003)

A new class of Conus peptides, the I-superfamily of conotoxins, has been characterized using biochemical, electrophysiological and molecular genetic methods. Peptides in this superfamily have a novel pattern of eight Cys residues. Five peptides that elicited excitatory symptomatology, r11a, r11b, r11c, r11d and r11e, were purified from Conus radiatus venom; four were tested on amphibian peripheral axons and shown to elicit repetitive action potentials, consistent with being members of the 'lightning-strike cabal' of toxins that effect instant immobilization of fish prey. A parallel analysis of Conus cDNA clones revealed a new class of conotoxin genes that was particularly enriched (with 18 identified paralogues) in a Conus radiatus venom duct library; several C. radiatus clones encoded the excitatory peptides directly characterized from venom. The remarkable diversity of related I-superfamily peptides within a single Conus species is unprecedented. When combined with the excitatory effects observed on peripheral circuitry, this unexpected diversity suggests a corresponding molecular complexity of the targeted signaling components in peripheral axons; the I-conotoxin superfamily should provide a rich lode of pharmacological tools for dissecting and understanding these. Thus, the I-superfamily conotoxins promise to provide a significant new technology platform for dissecting the molecular components of axons.
Role of mast cell chymase in excessive wound-healing response to vascular injury. (1994)

This study has analyzed the pathogenetic mechanism of the intimal thickening after baloon injury, which is currently a serious problem on the balloon angioplasty for coronary arteriosclerosis, from the aspect of wound-healing inflammation. The locally generated angiotensin II (AII), which is known for its aggravating effect on vascular hypertrophy, has been implicated to participate in the pathogenic mechanism. One month after the balloon injury, dog arteries showed myointimal hyperplasia as well as the increases in AII and AII-generating enzymes, angiotensin-converting enzyme and mast cell chymase, with the latter enzyme increasing more markedly. In the adventitia of lesioned vessels, the density of mast cells and fibrolasts was increased with apparent fibrosis and angiogenesis. These pathohistological findings suggest that the adventitial fibrosis reflects an excessive woundhealing response to the injury, and that the mast cell-fibroblast cross-talk may couple the adventitial fibrosis with the intimal hyperplasia. In this hyperplastic lesion, mast cell chymase seems to play a pivotal role by generating AII, and also by chymase's proinflammatory actions which are not yet fully defined. Thus, it is reasonable to regard the intimal thickening as a manifestation of exaggerated wound-healing response to an injury.
Synthetic strategies for 2,4-dimethoxypyrrolo[3,2-d]pyrimidine (1983)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTSynthetic strategies for 2,4-dimethoxypyrrolo[3,2-d]pyrimidineThomas L. Cupps, Dean S. Wise, and Leroy B. TownsendCite this: J. Org. Chem. 1983, 48, 7, 1060–1064Publication Date (Print):April 1, 1983Publication History Published online1 May 2002Published inissue 1 April 1983https://pubs.acs.org/doi/10.1021/jo00155a026https://doi.org/10.1021/jo00155a026research-articleACS PublicationsRequest reuse permissionsArticle Views381Altmetric-Citations23LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose Get e-Alerts
An algorithm to sculpt photon dispersion in a subwavelength nanostructure (2009)

We introduce a method of gradient-based optimization that continuously deforms a periodic dielectric distribution to generate photonic structures that possess any desired figure of merit expressible in terms of the electromagnetic eigenmodes. As an example, we generate forbidden regions between specified bands at extremely low dielectric contrast.
Theoretical analysis of the multicopy sampling method in molecular modeling (1993)

Langevin Monte Carlo dynamics and equilibrium properties of the multicopy sampling approximation in the modeling of ligand–protein complexes are studied. A perturbation form is derived based on the normal mode analysis, and can be used as a quantitative means to estimate the approximation prior to running a multicopy simulation. The multicopy dynamics is shown to induce an average dynamics of the protein and all the ligand copies, resulting in a well-defined equilibrium with uniform temperature. The induced average dynamics and the equilibrium represent the desired physics of the multicopy approximation, and are extended to include heterogeneous ligand copies. Such an extension presents a natural way to incorporate biologically important information on evolution into energy-based molecular modeling of homologous proteins.