gebhart/patrepeval huggingface dataset:
Biochemical characteristics and clinical applications of alpha-fetoprotein isoforms. (1995)

Alphafetoprotein (AFP) is an oncofetal glycoprotein that frequently reappears in sera of patients affected by hepatocellular carcinoma (HCC) and yolk-sac tumours (YST). In these cases AFP determination represents a useful marker for monitoring the therapeutic response and the clinical evolution of the neoplastic disease. AFP is a heterogeneous molecule with respect to the carbohydrate moiety and the different AFP glycoforms can be separated and characterized by their affinity for lectins, such as Concanavalin A (con A), and Lens culinaris agglutinin (LCA). Increased production of LCA-reactive AFP has been proposed as a specific and early marker for HCC, while Con A non-reactive AFP could be a marker for YST and gastrointestinal malignancies. In this review the molecular basis of AFP microheterogeneity and the clinical application of AFP isoforms will be discussed.
Molecular cloning of a highly repeated DNA element from Mycobacterium tuberculosis and its use as an epidemiological tool (1992)

In order to develop a technique for distinguishing between isolates of Mycobacterium tuberculosis, we cloned two hypervariable DNA fragments from NdeII-digested genomic DNA. The cloned DNA fragments of 3.8 and 4.7 kb were found to contain the same repetitive element, which was different from previously characterized repetitive elements. It is present in at least 30 copies per genome and is distributed among mycobacterial species other than those of the tuberculosis complex, including M. kansaii, M. gastri, and M. szulgai. When used as a probe on restriction enzyme-digested DNA, it can distinguish between strains from unrelated cases of tuberculosis while demonstrating identical banding patterns for isolates from epidemiologically related cases.
First 18F-Labeled Tracer Suitable for Routine Clinical Imaging of sst Receptor-Expressing Tumors Using Positron Emission Tomography (2004)

Due to the fast and high-yield chemoselective radiofluorination strategy and to its excellent pharmacokinetics, Cel-S-Dpr([(18)F]FBOA)TOCA represents the first tracer suitable for routine clinical application in PET somatostatin receptor imaging.
Tumor necrosis factor. (1976)

A century ago it was noted that a bacterial infection sometimes causes the regression of cancer. In 1975 the author found an explanation: the infection stimulates the secretion of tumor necrosis factor (TNF), which has anticancer activity. Now TNF, an important regulator of inflammation and immunity, is in clinical trials as an anticancer drug.
Ionic Field Effect Transistors with Sub-10 nm Multiple Nanopores (2009)

We report a new method to fabricate electrode-embedded multiple nanopore structures with sub-10 nm diameter, which is designed for electrofluidic applications such as ionic field effect transistors. Our method involves patterning pore structures on membranes using e-beam lithography and shrinking the pore diameter by a self-limiting atomic layer deposition process. We demonstrate that 70-80 nm diameter pores can be shrunk down to sub-10 nm diameter and that the ionic transport of KCl electrolyte can be efficiently manipulated by the embedded electrode within the membrane.
Comparison and evaluation of methods for generating differentially expressed gene lists from microarray data (2006)

We report that the choice of feature selection method, the number of genes in the genelist, the number of cases (samples) and the noise in the dataset, substantially influence classification success. Recommendations are made for choice of feature selection. Area under a ROC curve performed well with datasets that had low levels of noise and large sample size. Rank products performs well when datasets had low numbers of samples or high levels of noise. The Empirical bayes t-statistic performed well across a range of sample sizes.
Calcium‐dependent protein–protein interactions induce changes in proximity relationships of Cys48 and Cys64 in chicken skeletal troponin I (2003)

The goal of this study was to relate conformational changes in the N-terminal domain of chicken troponin I (TnI) to Ca2+ activation of the actin-myosin interaction. The two cysteine residues in this region (Cys48 and Cys64) were labeled with two sulfhydryl-reactive pyrene-containing fluorophores [N-(1-pyrene)maleimide, and N-(1-pyrene)iodoacetamide]. The labeled TnI showed a typical fluorescence spectrum: two sharp peaks of monomer fluorescence and a broad peak of excimer fluorescence arising from the formation of an excited dimer (excimer). Results obtained show that forming a binary complex of labeled TnI with skeletal TnC (sTnC) in the absence of Ca2+ decreases the excimer fluorescence, indicating a separation of the two residues. This reduction in excimer fluorescence does not occur when labeled TnI is complexed with cardiac TnC (cTnC). The latter causes only partial activation of the Ca2+-dependent myofibrillar ATPase. The binding of Ca2+ to the two N-terminal sites of sTnC causes a significant decrease in excimer fluorescence and an increase in monomer fluorescence in complexes of labeled TnI with skeletal TnC or TnC/TnT, while Ca2+ binding to site II of cTnC only causes an increase in monomer fluorescence but no change in excimer fluorescence. Thus a conformational change in the N-terminal region of TnI may be necessary for full activation of muscle contraction.
Haemolytic disease of the fetus and newborn due to anti‐Fya and the potential clinical value of Duffy genotyping in pregnancies at risk (1997)

Haemolytic disease of the newborn (HDN) caused by anti-Fy(a) is uncommon and usually mild. Current guidelines recommend that pregnant women with anti-Fy(a) are monitored less rigorously than those with anti-D, -c or -K. However, in a review of our recent experience of 68 pregnancies where anti-Fy(a) was detected, three were identified where the fetus was severely anaemic; in two cases the fetus received intrauterine transfusions. Our data suggest that pregnancies in which anti-Fy(a) is detected at significant titres (> 64) should be closely monitored in a similar way to pregnancies where other 'significant' antibodies are present. Moreover, in the presence of high or rising antibody titres, if the father is heterozygous and functional assays suggest the antibody is active, then fetal genotyping should be offered to help plan the future management of that pregnancy.
Evidence for Direct Interaction between Sprouty and Cbl (2001)

Sprouty (SPRY) was first identified in a genetic screen in Drosophila as an antagonist of fibroblast and epidermal growth factor receptors and Sevenless signaling, seemingly by inhibiting the receptor tyrosine kinase (RTK)/Ras/MAPK pathway. To date, four mammalian Sprouty genes have been identified; the primary sequences of the gene products share a well conserved cysteine-rich C-terminal domain with their Drosophila counterpart. The N-terminal regions do not, however, exhibit a large degree of homology. This study was aimed at identifying proteins with which human SPRY2 (hSPRY2) interacts in an attempt to understand the mechanism by which Sprouty proteins exert their down-regulatory effects. Here, we demonstrate that hSPRY2 associates directly with c-Cbl, a known down-regulator of RTK signaling. A short sequence in the N terminus of hSPRY2 was found to bind directly to the Ring finger domain of c-Cbl. Parallel binding was apparent between the Drosophila homologs of Sprouty and Cbl, with cross-species associations occurring at least in vitro. Coexpression of hSPRY2 abrogated an increase in the rate of epidermal growth factor receptor internalization induced by c-Cbl, whereas a mutant hSPRY2 protein unable to bind c-Cbl showed no such effect. Our results suggest that one function of hSPRY2 in signaling processes downstream of RTKs may be to modulate c-Cbl physiological function such as that seen with receptor-mediated endocytosis.
Logical vs. physical file system backup (1999)

As file systems grow in size, ensuring that data is safely stored becomes more and more difficult. Historically, file system backup strategies have focused on logical backup where files are written in their entirety to the backup media. An alternative is physical backup where the disk blocks that make up the file system are written to the backup media. This paper compares logical and physical backup strategies in large file systems. We discuss the advantages and disadvantages of the two approaches, and conclude by showing that while both can achieve good performance, physical backup and restore can achieve much higher throughput while consuming less CPU. In addition, physical backup and restore is much more capable of scaling its performance as more devices are added to a system.
Suppressor cel activity of ferritin-bearing lymphocytes in patients with breast cancer. (1982)

In patients with early stages (I, II) of breast cancer we identified a subset of circulating lymphocytes that carry ferritin on their surface. No such lymphocytes were identified in normal women nor in women with benign breast disease. These cells did not form spontaneous rosettes with sheep red blood cells. Further studies revealed that in vitro treatment of the patients' lymphocytes with levamisole resulted n the removal of the surface ferritin and in an increase in the reactivity of the lymphocytes in mixed lymphocyte culture (MLC). Separation of the ferritin-positive lymphocytes from the E-rosetting T cells resulted in an increased reactivity of the patients' T cells in MLC. Readdition of the fraction containing the ferritin-positive cells to a mixed lymphocyte culture resulted in a decrease in the proliferative response of the patients' T lymphocytes. It is suggested that the ferritin-positive lymphocytes in breast cancer patients represent an active suppressor cell subset.
Bacterial Interactions in Dental Biofilm Development (2009)

Recent analyses with ribosomal RNA-based technologies have revealed the diversity of bacterial populations within dental biofilms, and have highlighted their important contributions to oral health and disease. Dental biofilms are exceedingly complex and multispecies ecosystems, where oral bacteria interact cooperatively or competitively with other members. Bacterial interactions that influence dental biofilm communities include various different mechanisms. During the early stage of biofilm formation, it is known that planktonic bacterial cells directly attach to surfaces of the oral cavity or indirectly bind to other bacterial cells that have already colonized. Adherence through co-aggregation may be critical for the temporary retention of bacteria on dental surfaces, and may facilitate eventual bacterial colonization. It is likely that metabolic communication, genetic exchange, production of inhibitory factors (e.g., bacteriocins, hydrogen peroxide, etc.), and quorum-sensing are pivotal regulatory factors that determine the bacterial composition and/or metabolism. Since each bacterium can easily access a neighboring bacterial cell and its metabolites, genetic exchanges and metabolic communication may occur frequently in dental biofilms. Quorum-sensing is defined as gene regulation in response to cell density, which influences various functions, e.g., virulence and bacteriocin production. In this review, we discuss these important interactions among oral bacteria within the dental biofilm communities.
A novel family of cell surface receptors with tyrosine kinase-like domain. (1992)

Human cDNA clones encoding two novel proteins with a region strongly homologous to the tyrosine kinase domain of growth factor receptors, in particular of the Trk family, were obtained by a polymerase chain reaction-based approach. These proteins, Ror1 and Ror2, share 58% overall amino acid identity and a structure indicative of cell surface molecules. A secretion signal sequence and a transmembrane domain delimit the extracellular portion, which contains immunoglobulin-like, cysteine-rich, and kringle domains. The cytoplasmic portion contains the tyrosine kinase-like domain which (in Ror2) appears to be associated with protein kinase activity in vitro, followed by serine/threonine- and proline-rich motifs. Partial nucleotide sequences of the rat genes reveal striking evolutionary conservation of the proteins between human and rat. The level of expression of the rat genes is high in the head and body of early embryo and decreases dramatically after embryonic day 16. Based on these data, Ror1 and Ror2 appear to define a new developmentally regulated family of cell surface receptors for unidentified ligands.
Virulence and immunogenicity of a temperature-sensitive dengue-2 virus in lower primates (1977)

Clones of dengue-2 virus were tested for virulence by inoculation of rhesus monkeys and chimpanzees. Although primates showed no overt signs of illness, inoculation with the parent virus or a subline of a large-plaque clone resulted in a viremia lasting 1 to 7 days. By these criteria, sublines of a small-plaque clone were significantly less virulent and produced little or no viremia in primate hosts. Although they had a substantially reduced viremia, primates inoculated with the small-plaque sublines showed stimulation of complement-fixing, hemagglutination-inhibiting, and neutralizing antibodies. The protection afforded rhesus monkeys 3 months after inoculation with two of the small-plaque sublines was demonstrated by a lack of viremia and a failure to escalate preexisting antibody levels after challenge with the parent virus. Both the S-1 subline and the parent virus had a limited capacity to produce central nervous system pathology in monkeys inoculated intrathalamically and intrathecally. Evidence thus far accumulated for primates indicates that the S-1 subline of dengue-2 virus has potential value as a candidate vaccine virus.
Understanding the Fundamentals of Perfluorocarbons and Perfluorocarbon Emulsions Relevant toIn VivoOxygen Delivery (2005)

The unique behavior of perfluorocarbons (PFCs), including their high oxygen dissolving capacity, hydrophobic and lipophobic character, and extreme inertness, derive directly, in a predictable manner, from the electronic structure and spatial requirements of the fluorine atom. Their low water solubility is key to the prolonged in vivo persistence of the now commercially available injectable microbubbles that serve as contrast agents for diagnostic ultrasound imaging. OxygentTM, a stable, small-sized emulsion of a slightly lipophilic, rapidly excreted PFC, perfluorooctyl bromide (perflubron), has been engineered. Significant oxygen delivery has been established in animal models and through Phase II and III human clinical trials. However, an inappropriate testing protocol and the lack of funding led to temporary suspension of the trials.
Control of Flow Direction in Microfluidic Devices with Polyelectrolyte Multilayers (2000)

Electroosmotic flow (EOF) is commonly utilized in microfluidics. Because the direction of the EOF can be determined by the substrate surface charge, control of the surface chemical state offers the potential, in addition to voltage control, to direct the flow in microfluidic devices. We report the use of polyelectrolyte multilayers (PEMs) to alter the surface charge and control the direction of flow in polystyrene and acrylic microfluidic devices. Relatively complex flow patterns with simple arrangements of applied voltages are realized by derivatization of different arms of a single device with oppositely charged polyelectrolytes. In addition, flow in opposite directions in the same channel is possible. A positively derivatized plastic substrate with a negatively charged lid was used to achieve top-bottom opposite flows. Derivatization of the two sides of a plastic microchannel with oppositely charged polyelectrolytes was used to achieve side-by-side opposite flows. The flow is characterized using fluorescence imaging and particle velocimetry.
Oxygenation of ferrous ions in reversed micelle and reversed microemulsion (1982)

ADVERTISEMENT RETURN TO ISSUEPREVArticleNEXTOxygenation of ferrous ions in reversed micelle and reversed microemulsionKatsuya Inouye, Rieko Endo, Yoko Otsuka, Keiko Miyashiro, Katsumi Kaneko, and Tatsuo IshikawaCite this: J. Phys. Chem. 1982, 86, 8, 1465–1469Publication Date (Print):April 1, 1982Publication History Published online1 May 2002Published inissue 1 April 1982https://pubs.acs.org/doi/10.1021/j100397a051https://doi.org/10.1021/j100397a051research-articleACS PublicationsRequest reuse permissionsArticle Views311Altmetric-Citations57LEARN 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 options Get e-Alerts
Preliminary deep water results in single-beacon one-way-travel-time acoustic navigation for underwater vehicles (2009)

This paper reports the development and experimental evaluation of a novel navigation system for underwater vehicles that employs Doppler sonar, synchronous clocks, and acoustic modems to achieve simultaneous acoustic communication and navigation. The system reported herein, which is employed to renavigate the vehicle in post-processing, forms the basis for a vehicle-based real-time navigation system. Existing high-precision absolute navigation techniques for underwater vehicles are impractical over long length scales and lack scalability for simultaneously navigating multiple vehicles. The navigation method reported in this paper relies on a single moving reference beacon, eliminating the requirement for the underwater vehicle to remain in a bounded navigable area. The use of underwater modems and synchronous clocks enables range measurements based on one-way time-of-flight information from acoustic data packet broadcasts. The acoustic data packets are broadcast from the single, moving reference beacon and can be received simultaneously by multiple vehicles within acoustic range. We report experimental results from the first deep-water evaluation of this method using data collected from an autonomous underwater vehicle (AUV) survey carried out in 4000 m of water on the southern Mid-Atlantic Ridge. We report a comparative experimental evaluation of the navigation fixes provided by the proposed synchronous acoustic navigation system in comparison to navigation fixes obtained by an independent conventional long baseline acoustic navigation system.
Specification of embryonic axes begins before cleavage in normal mouse development (2001)

Studies on the development of aggregated, isolated and rearranged blastomeres have engendered the view that in mammals, unlike most other animals, egg organization has no role in the genesis of asymmetries that are essential for cellular diversification and the specification of embryonic axes. Such asymmetries are assumed to arise post-zygotically through interactions between initially naive cells. However, various findings are difficult to reconcile with this view. Here, a consistent relationship between the structure of the blastocyst and the two-cell stage in the mouse has been found using a strictly non-invasive marking technique: injection of small oil drops into the substance of the zona pellicuda. This has revealed that both the embryonic-abembryonic axis of the blastocyst and its plane of bilateral symmetry are normally orthogonal to the plane of first cleavage. This relationship was also seen when denuded two-cell conceptuses were prevented from rotating during subsequent cleavage by immobilizing them in a gel. Therefore, during normal mouse development the axes of the blastocyst, which have been implicated in establishing those of the fetus, are already specified by the onset of cleavage.
Cdc25 Mitotic Inducer Targeted by Chk1 DNA Damage Checkpoint Kinase (1997)

Arrest of the cell cycle at the G2 checkpoint, induced by DNA damage, requires inhibitory phosphorylation of the kinase Cdc2 in both fission yeast and human cells. The kinase Wee1 and the phosphatase Cdc25, which regulate Cdc2 phosphorylation, were evaluated as targets of Chk1, a kinase essential for the checkpoint. Fission yeast cdc2-3w Deltacdc25 cells, which express activated Cdc2 and lack Cdc25, were responsive to Wee1 but insensitive to Chk1 and irradiation. Expression of large amounts of Chk1 produced the same phenotype as did loss of the cdc25 gene in cdc2-3w cells. Cdc25 associated with Chk1 in vivo and was phosphorylated when copurified in Chk1 complexes. These findings identify Cdc25, but not Wee1, as a target of the DNA damage checkpoint.
Interaction of bovine coagulation factor X and its glutamic‐acid‐containing fragments with phospholipid membranes (2002)

The interaction of blood coagulation factor X and its Gla-containing fragments with negatively charged phospholipid membranes composed of 25 mol% phosphatidylserine (PtdSer) and 75 mol% phosphatidylcholine (PtdCho) was studied by surface plasmon resonance. The binding to 100 mol% PtdCho membranes was negligible. The calcium dependence in the membrane binding was evaluated for intact bovine factor X (factor X) and the fragment containing the Gla-domain and the N-terminal EGF (epidermal growth factor)-like domain, Gla-EGFN, from factor X. Both proteins show the same calcium dependence in the membrane binding. Calcium binding is cooperative and half-maximum binding was observed at 1.5 mm and 1.4 mm, with the best fit to the experimental data with three cooperatively bound calcium ions for both the intact protein and the fragment. The dissociation constant (Kd) for binding to membranes containing 25 mol% PtdSer decreased from 4.6 microm for the isolated Gla-domain to 1 microm for the fragments Gla-EGFN and Gla-EGFNC (the Gla-domain and both EGF-like domains) fragments and to 40 nm for the entire protein as zymogen, activated enzyme or in the active-site inhibited form. Analysis of the kinetics of adsorption and desorption confirmed the equilibrium binding data.
Micro- and Nanostructured Surface Morphology on Electrospun Polymer Fibers (2002)

Electrospun fibers were produced using a variety of solvents to investigate the influence of polymer/solvent properties on the fiber surface morphology. Electrospinning is a novel processing technique for the production of fibers with diameters in the range of a few nanometers to tens of micrometers. We have been able to produce polymeric fibers with a high surface area through the introduction of a micro- and nanostructured surface structure, which we refer to as a “porous” morphology. These features could be introduced in several different polymeric fibers increasing their range of application significantly. The pores vary from densely packed, well-formed nanopores with diameters in the range 20−350 nm to larger flat pores of about 1 μm. The increased surface area of polymeric fibers was correlated with high volatility solvents used in the electrospinning process. The effect of processing parameters on the fiber surface morphology was also investigated using optical microscopy, field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), and atomic force microscopy (AFM).