gebhart/patrepeval huggingface dataset:
Evidence for plasmid-mediated toxin production in Bacillus anthracis (1983)

Large-molecular-weight plasmids were isolated from virulent and avirulent strains of Bacillus anthracis. Each strain contained a single plasmid species unique from the others with respect to molecular weight. Bacterial strains were cured of their resident extrachromosomal gene pools by sequential passage of cultures at 42.5 degrees C. Coincidental to the curing of plasmids was a loss of detectable lethal toxin and edema-producing activities and a dramatic decrease in lethal factor and protective antigen serological activities. The involvement of these plasmids in the production of toxin was firmly established by transformation of heat-passaged cells with plasmid DNA purified from the parent strain. The ability to produce parent strain levels of toxin was restored, and the plasmid DNA similar in molecular weight to that isolated from the parent was reisolated in all transformants examined. The exact role these plasmids play in the production of toxin remains to be elucidated. Two additional strains of B. anthracis, designated Pasteur vaccine strains, were examined for the ability to produce toxin and for the presence of plasmid DNA. Both strains were found to be nontoxigenic and contained no detectable plasmid elements. It is therefore likely that we, like Pasteur, cured B. anthracis strains of temperature-sensitive plasmids which code for toxin structural or regulatory proteins.
[Clinical study on effect of Shenyin Oral Liquid in treating mild cognitive impairment]. (2007)

SOL has an effect similar to cholinesterase inhibitor, it could improve cognitive function in MCI patients and reduce the AD transformation rate in them.
Clinical Experience with Angiotensin II in the Treatment of Shock (1961)

The effects of using angiotensin in the treatment of shock from various causes were studied in 21 patients. The blood pressure returned to normal in every instance excepting 6 patients who were moribund when treatment was begun. Of 6 patients who were in advanced bacteremic shock and whose prognosis was considered hopeless, 4 survived as did one with severe shock associated with postoperative intracranial bleeding and two with severe barbiturate poisoning. Angiotensin was also used in treating 10 patients in whom hypotension appeared in the course of dialysis by an artificial kidney. Six survived. In this series of cases angiotensin produced no side effects of any sort.
Trust in Information Visualization (2019)

Trust is an important factor that mediates whether a user will rely and build on the information displayed in a visualization. Research in other fields shows that there are different mechanisms of trust building: Users might elaborate the information deeply and gain a good understanding of the uncertainties in the data and quality of the information. But they might also use superficial cues as indicators for trust. Which processes are activated depends on the trustworthiness on the side of the visualization and on the trust perception by the users. We lay out challenges for future research to further improve our understanding of trust in information visualization.
Protein Kinase C Regulation of Intracellular and Cell Surface Amyloid Precursor Protein (APP) Cleavage in CHO695 Cells (2000)

Cleavage of amyloid precursor protein (APP) by beta-secretase generates beta-amyloid (Abeta), the major component of senile plaques in Alzheimer's disease. Cleavage of APP by alpha-secretase prevents Abeta formation, producing nonamyloidogenic secreted APPs products. PKC-regulated APP alpha-secretase cleavage has been shown to involve tumor necrosis factor alpha (TNF-alpha) converting enzyme (TACE). To determine the location of APP cleavage, we examined PKC-regulated APPs secretion by examining cell surface versus intracellular APP in CHO cells stably expressing APP(695) (CHO695). We demonstrate that PKC regulates cell surface and intracellular APP cleavage. The majority of secreted APPs originates from the intracellular compartment, and PKC does not cause an increase in APP trafficking to the cell surface for cleavage. Therefore, intracellular APP regulated by PKC must be cleaved at an intracellular site. Experiments utilizing Brefeldin A suggest APP cleavage occurs at the Golgi or late in the secretory pathway. Experiments using TAPI, an inhibitor of TACE, demonstrate PKC-regulated APPs secretion from the cell surface is inhibited after pretreatment with TAPI, and APPs secretion from the intracellular pool is partially inhibited after pretreatment with TAPI. These findings suggest PKC-regulated APP cleavage occurs at multiple locations within the cell and both events appear to involve TACE.
Journal of Hematology & Oncology reviewer acknowledgement 2012 (2013)

The editor of Journal of Hematology & Oncology would like to thank all our reviewers who have contributed to the journal in Volume 5 (2012).
Endothelial leukocyte adhesion molecule 1: direct expression cloning and functional interactions. (1990)

A cDNA for endothelial leukocyte adhesion molecule 1 (ELAM-1) was isolated by transient expression in COS-7 cells of a subtracted cDNA library from cytokine-treated human umbilical vein endothelial cells (HUVECs), with selection of ELAM-1-expressing clones by adhesion of transfected cells to the human promyelocytic cell line HL-60. This cloning method requires neither antibody nor purified ligand. ELAM-1-expressing COS cells bind the promyelocytic cell line HL-60 by a Ca2(+)-dependent but temperature-independent mechanism. Although ELAM-1 is homologous to mammalian lectins, its interaction with HL-60 cells is not inhibited by simple carbohydrate structures. ELAM-1-expressing COS cells also bind human neutrophils and the human colon carcinoma cell line HT-29, but not the B-cell line Ramos. However, Ramos cells adhere to cytokine-treated HUVECs but not control HUVECs, confirming the existence of other inducible adhesion molecules. In addition, the binding of HL-60 cells or neutrophils to ELAM-1-expressing COS cells is not inhibited by a monoclonal antibody (60.3) directed to an inhibitory epitope on CD18, indicating that the ELAM-1 ligand, although uncharacterized, is not a member of the CD11/CD18 family.
Human actin genes are single copy for alpha-skeletal and alpha-cardiac actin but multicopy for beta- and gamma-cytoskeletal genes: 3' untranslated regions are isotype specific but are conserved in evolution. (1983)

We have constructed isotype-specific subclones from the 3' untranslated regions of alpha-skeletal, alpha-cardiac, beta-cytoskeletal, and gamma-cytoskeletal actin cDNAs. These clones have been used as hybridization probes to assay the number and organization of these actin isotypes in the human genome. Hybridization of these probes to human genomic actin clones (Engel et al., Proc. Natl. Acad. Sci. U.S.A. 78:4674-4678, 1981; Engel et al., Mol. Cell. Biol. 2:674-684, 1982) has allowed the unambiguous assignment of the genomic clones to isotypically defined actin subfamilies. In addition, only one isotype-specific probe hybridizes to each actin-containing gene, with a single exception. This result suggests that the multiple actin genes in the human genome are not closely linked. Genomic DNA blots probed with these subclones under stringent conditions demonstrate that the alpha-skeletal and alpha-cardiac muscle actin genes are single copy, whereas the cytoskeletal actins, beta and gamma, are present in multiple copies in the human genome. Most of the actin genes of other mammals are cytoplasmic as well. These observations have important implications for the evolution of multigene families.
S100 proteins and their influence on pro-survival pathways in cancer (2004)

The S100 gene family is composed of at least 20 members that share a common structure defined in part by the Ca 2+ binding EF-hand motif. These genes which are expressed in a discriminate fashion in specific cells and tissues, have been described to have either an intracellular or extracellular function, or both. S100 proteins are implicated in the immune response, differentiation, cytoskeleton dynamics, enzyme activity, Ca 2+ homeostasis and growth. A potential role for S100 proteins in neoplasia stems from these activities and from the observation that several S100 proteins have altered levels of expression in different stages and types of cancer. While the precise role and importance of S100 proteins in the development and promotion of cancer is poorly understood, it appears that the binding of Ca 2+ is essential for exposing amino acid residues that are important in forming protein-protein interactions with effector molecules. The identity of some of these effector molecules has also now begun to emerge, and with this the elucidation of the signaling pathways that are modulated by these proteins. Some of these interactions are consistent with the diverse functions noted above. Others suggest that, many S100s may also promote cancer progression through specific roles in cell survival and apoptosis pathways. This review summarizes these findings and their implications.
HIV-1 infection and pathogenesis in a novel humanized mouse model (2006)

The Rag2-gammaC double-knockout (DKO) mouse lacks T, B, and natural killer (NK) cells, and allows development of a functional human immune system with human CD34+ hematopoietic stem/progenitor cells (DKO-hu HSCs). Normal human T, B, and dendritic cells are present in peripheral blood, thymus, spleen, and lymph nodes. We report that both CCR5 and CXCR4 are expressed on human immature and mature T cells. DKO-hu HSC mice allow efficient HIV-1 infection with plasma high viremia. High levels of productive infection occur in the thymus, spleen, and lymph nodes. Human CD4+ T cells are gradually depleted by HIV-1 in a dose-dependent manner. In addition, HIV-1 infection persists in infected DKO-hu HSC mice for at least 19 weeks, with infectious HIV-1 in lymphoid tissues. Thus, the DKO-hu HSC mouse can serve as a relevant in vivo model to investigate mechanisms of HIV-1 infection and immunopathogenesis as well as to develop anti-HIV-1 therapeutics.
G-Protein Coupled Receptors as Allosteric Machines (2004)

Allosterism, whereby small molecule ligands produce global changes in the conformations of receptors, is a powerful mechanism for drug effect. This is illustrated by the recent data describing CCR5 antagonists as blockers of HIV infection. Allosteric effects are described in terms of a change in the tertiary conformation of the receptor. This paper outlines some unique features of allosteric antagonists as new drug entities. These include the fact that allosteric ligands have texture in antagonism (not all allosterically blocked receptors are alike), allosteric blockade is probe dependent (not all agonists and radioligands are blocked equally), and the fact that allosteric binding involves a separate site on the receptor may have relevance to duration of effect and selectivity. Dissociation between receptor function and binding also can be encountered with allosteric ligands.
An O-Plate Compensated In-Plane Switching Liquid Crystal Display (2006)

Pretilt angle effect on the dark-state light leakage and viewing angle of in-plane switching (IPS) liquid crystal display is investigated. As the liquid crystal (LC) pretilt angle increases, the light leakage becomes more severe and the off-axis light leakage from the out-of-plane LC directors cannot be neglected. Introducing an oblique compensation plate (O-plate) reduces the off-axis light leakages from the crossed linear polarizers and the anisotropic LC media simultaneously which, in turn, improves the viewing angle of the IPS LCD.
111In-Labeled Lactam Bridge-Cyclized α-Melanocyte Stimulating Hormone Peptide Analogues for Melanoma Imaging (2008)

The purpose of this study was to examine the influence of the lactam bridge cyclization on melanoma targeting and biodistribution properties of the radiolabeled conjugates. Two novel lactam bridge-cyclized alpha-MSH peptide analogues, DOTA-CycMSH (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid-c[Lys-Nle-Glu-His-DPhe-Arg-Trp-Gly-Arg-Pro-Val-Asp]) and DOTA-GlyGlu-CycMSH (DOTA-Gly-Glu-c[Lys-Nle-Glu-His-DPhe-Arg-Trp-Gly-Arg-Pro-Val-Asp]), were synthesized and radiolabeled with (111)In. The internalization and efflux of (111)In-labeled CycMSH peptides were examined in B16/F1 melanoma cells. The melanoma targeting properties, pharmacokinetics, and SPECT/CT imaging of (111)In-labeled CycMSH peptides were determined in B16/F1 melanoma-bearing C57 mice. Both (111)In-DOTA-CycMSH and (111)In-DOTA-GlyGlu-CycMSH exhibited fast internalization and extended retention in B16/F1 cells. The tumor uptake values of (111)In-DOTA-CycMSH and (111)In-DOTA-GlyGlu-CycMSH were 9.53+/-1.41% injected dose/gram (% ID/g) and 10.40+/-1.40% ID/g at 2 h postinjection, respectively. Flank melanoma tumors were clearly visualized with (111)In-DOTA-CycMSH and (111)In-DOTA-GlyGlu-CycMSH by SPECT/CT images at 2 h postinjection. Whole-body clearance of the peptides was fast, with greater than 90% of the radioactivities cleared through urinary system by 2 h postinjection. There was low radioactivity (<0.8% ID/g) accumulated in blood and normal organs except kidneys at all time points investigated. Introduction of a negatively charged linker (-Gly-Glu-) into the peptide sequence decreased the renal uptake by 44% without affecting the tumor uptake at 4 h postinjection. High receptor-mediated melanoma uptakes coupled with fast whole-body clearance in B16/F1 melanoma-bearing C57 mice demonstrated the feasibility of using (111)In-labeled lactam bridge-cyclized alpha-MSH peptide analogues as a novel class of imaging probes for receptor-targeting melanoma imaging.
Microfluidic device with carbon nanotube channel walls for blood plasma extraction (2013)

The human plasma biomarker analysis is promised to be a revolution for disease diagnosis and therapeutic monitoring, but it also presents major technical challenges that needs to be addressed [1]. Plasma extract from whole blood is the first step for plasma biomarker analysis. This paper reports a new microfluidic device with channel walls made of nitrogen-doped carbon nanotubes (CNxCNT) as a point-of-care device to continuously extract plasma from human whole blood. The cross flow microfiltration principle is applied in this plasma extraction device. The blood sample is transported within the double spiral channels. The plasma diffuses through the porous CNxCNT wall into the spiral plasma channel while blood cells continue to flow inside the spiral blood sample channel [2].
Biomaterial-Centered Infection: Microbial Adhesion Versus Tissue Integration (1987)

Biomaterials are being used with increasing frequency for tissue substitution. Complex devices such as total joint replacements and the total artificial heart represent combinations of polymers and metal alloys for system and organ replacement. The major barriers to the extended use of these devices are the possibility of bacterial adhesion to biomaterials, which causes biomaterial-centered infection, and the lack of successful tissue integration or compatibility with biomaterial surfaces. Interactions of biomaterials with bacteria and tissue cells are directed not only by specific receptors and outer membrane molecules on the cell surface, but also by the atomic geometry and electronic state of the biomaterial surface. An understanding of these mechanisms is important to all fields of medicine and is derived from and relevant to studies in microbiology, biochemistry, and physics. Modifications to biomaterial surfaces at an atomic level will allow the programming of cell-to-substratum events, thereby diminishing infection by enhancing tissue compatibility or integration, or by directly inhibiting bacterial adhesion.
Shape-based analysis of right ventricular dysfunction associated with acute pulmonary embolism (2012)

Acute pulmonary embolism (APE) is known as one of the major causes of sudden death. However, high level of mortality caused by APE can be reduced, if detected in early stages of development. Hence, biomarkers capable of early detection of APE are of utmost importance. This study investigates how APE affects the biomechanics of the cardiac right ventricle (RV), taking one step towards developing functional biomarkers for early diagnosis and determination of prognosis of APE. To that end, we conducted a pilot study in pigs, which revealed the following major changes due to the severe RV afterload caused by APE: (1) waving paradoxical motion of the RV inner boundary, (2) decrease in local curvature of the septum, (3) lower positive correlation between the movement of inner boundaries of the septal and free walls of the RV, (4) slower blood ejection by the RV, and (5) discontinuous movement observed particularly in the middle of the RV septal wall.
Big Data Analytics in Bioinformatics: A Machine Learning Perspective (2015)

Bioinformatics research is characterized by voluminous and incremental datasets and complex data analytics methods. The machine learning methods used in bioinformatics are iterative and parallel. These methods can be scaled to handle big data using the distributed and parallel computing technologies. Usually big data tools perform computation in batch-mode and are not optimized for iterative processing and high data dependency among operations. In the recent years, parallel, incremental, and multi-view machine learning algorithms have been proposed. Similarly, graph-based architectures and in-memory big data tools have been developed to minimize I/O cost and optimize iterative processing. However, there lack standard big data architectures and tools for many important bioinformatics problems, such as fast construction of co-expression and regulatory networks and salient module identification, detection of complexes over growing protein-protein interaction data, fast analysis of massive DNA, RNA, and protein sequence data, and fast querying on incremental and heterogeneous disease networks. This paper addresses the issues and challenges posed by several big data problems in bioinformatics, and gives an overview of the state of the art and the future research opportunities.
DMSO-enhanced whole cell yeast transformation (1991)

Journal Article DMSO-enhanced whole cell yeast transformation Get access James Hill, James Hill Department of Chemistry, University of WarwickCoventry CV4 7AL, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar K.A.Ian G. Donald, K.A.Ian G. Donald Department of Chemistry, University of WarwickCoventry CV4 7AL, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar David E. Griffiths David E. Griffiths Department of Chemistry, University of WarwickCoventry CV4 7AL, UK Search for other works by this author on: Oxford Academic PubMed Google Scholar Nucleic Acids Research, Volume 19, Issue 20, 25 October 1991, Page 5791, https://doi.org/10.1093/nar/19.20.5791 Published: 25 October 1991 Article history Received: 22 August 1991 Published: 25 October 1991
Power-rate-distortion analysis for wireless video communication under energy constraints (2005)

Mobile devices performing video coding and streaming over wireless and pervasive communication networks are limited in energy supply. To prolong the operational lifetime of these devices, an embedded video encoding system should be able to adjust its computational complexity and energy consumption as demanded by the situation and its environment. To analyze, control, and optimize the rate-distortion (R-D) behavior of the wireless video communication system under the energy constraint, we develop a power-rate-distortion (P-R-D) analysis framework, which extends the traditional R-D analysis by including another dimension, the power consumption. Specifically, in this paper, we analyze the encoding mechanism of typical video coding systems, and develop a parametric video encoding architecture which is fully scalable in computational complexity. Using dynamic voltage scaling (DVS), an energy consumption management technology recently developed in CMOS circuits design, the complexity scalability can be translated into the energy consumption scalability of the video encoder. We investigate the R-D behavior of the complexity control parameters and establish an analytic P-R-D model. Both theoretically and experimentally, we show that, using this P-R-D model, the video coding system is able to automatically adjust its complexity control parameters to match the available energy supply of the mobile device while maximizing the picture quality. The P-R-D model provides a theoretical guideline for system design and performance optimization in mobile video communication under energy constraints.
Phase II preclinical drug screening in human tumor xenografts: a first European multicenter collaborative study. (1992)

In a European joint project carried out in 6 laboratories a disease-oriented program was set up consisting of a panel of 7 tumor types, each represented by 4 to 8 different human tumor lines, for secondary screening of promising anticancer drugs. Human tumor lines were selected on the basis of differences in histology, growth rate, and sensitivity to conventional cytostatic agents. Xenografts were grown s.c. in nude mice, and treatment was started when tumors reached a mean diameter of 6 mm in groups of mice where at least 6 tumors were evaluable. Drugs were given at the maximum tolerated dose. For evaluation of drug efficacy, median tumor growth curves were drawn, and specific growth delay and treated/control x 100% were calculated. Doxorubicin (8 mg/kg i.v. days 1 and 8) was effective (treated/control < 50%, and specific growth delay > 1.0) in 0 of 2 breast cancers, 1 of 3 colorectal cancers, 2 of 5 head and neck cancers, 3 of 6 non-small cell lung cancers, 4 of 6 small cell lung cancers, 0 of 3 melanomas, and 3 of 6 ovarian cancer lines. Amsacrine (8 mg/kg i.v. days 1 and 8) was not effective, while datelliptium (35 mg/kg i.p. days 1 and 8) was active against 2 of 6 small cell lung cancer lines. Brequinar sodium (50 mg/kg i.p. days 1-5) showed efficacy in 4 of 5 head and neck cancers, 5 of 8 non-small cell lung cancers, and 4 of 5 small cell lung cancer lines. The project has been shown to be a feasible approach. Clinical activity for doxorubicin and inactivity for amsacrine against solid tumor types was confirmed in the human tumor xenograft panel. Additional anticancer drugs will be studied in the European joint project to further define the reliability of this novel, promising screening approach.
Peptide mapping and microsequencing of proteins separated by SDS-PAGE after limited in situ acid hydrolysis. (1992)

A method is described for the isolation of peptide fragments from proteins separated by polyacrylamide gel electrophoresis. After completion of the electrophoresis step, gels are stained with Ponceau S or Coomassie Blue. Gel portions containing protein stained with Ponceau S are excised and transferred to borosilicate glass digestion tubes containing 0.9 ml of 1 mM NaOH or 5 mM Na2HPO4. After complete dissociation of the dye from the protein, 0.1 ml of 20% formic acid is added and the protein is hydrolyzed in situ at 112 degrees C for four hours. Subsequently the acid solution is made 10% in acetonitrile and chromatographed as such on a C18 (C4) reversed-phase column using an appropriate large-volume sample loading syringe and injection loop. Proteins stained with Coomassie Blue can be hydrolyzed in situ after complete removal of the dye with an aqueous solution containing 40% acetone, 10% triethylamine and 5% acetic acid. The gel slices are next washed with HPLC-grade water and protein is hydrolyzed in 2% formic acid under standard conditions. Gel-related contaminants do not interfere with the peptide separation under the proper conditions of HPLC analysis.