gebhart/patrepeval huggingface dataset:
Automatic data classification by a hierarchy of self-organizing maps (2003)

Clustering is the process by which discrete objects are assigned to groups that have similar characteristics. Self-organizing maps (SOM) have been widely used as a data visualization tool. Some of their advantages include information compression and density estimation while trying to preserve the topological and metric relationships of the primary data items. For using SOM as a clustering tool additional procedures are required to interpret the mapping obtained through unsupervised learning. Costa and Netto (1999) described the usage of image analysis and mathematical morphology to find automatically regions of similar neurons and their borders. The purpose of this paper is to enhance the clustering process in order to detail the underlying structure obtained in a first trial. Groups of neurons associated to clusters are further subdivided in new sub-networks, generating a tree-like structure of SOMs. Differently to other hierarchical SOM approaches, the number of sub-nets for a given SOM in a given height of the tree is not specified in advance. The process can be seen as a dynamic strategy for cluster discovery.
Cascade single-chip phosphor-free white light-emitting diodes (2008)

In order to resolve the problems existing in the conventional phosphor-converted light-emitting-diodes (LEDs) and red-green-blue LEDs, the cascade single-chip phosphor-free white LED was proposed with GaAs∕GaN heterojunction direct wafer bonding. Corresponding to the color-matching calculation, the white LED demonstrated the CIE chromaticity coordinates of about (0.3, 0.3) at 20mA, which was very close to the ideal white light position (1∕3, 1∕3) on the chromaticity diagram. The fabrication and the electrical and optical performances of such white LEDs were described.
Polarization volume grating with high efficiency and large diffraction angle (2016)

We propose a polarization volume grating (PVG), which exhibits nearly 100% diffraction efficiency and large diffraction angle. Both reflective and transmissive PVGs can be configured depending on application preference. Such a PVG is polarization-sensitive so that it can split an incident unpolarized beam into two well-separated yet polarized beams. These outstanding features make PVG a strong candidate for photonic and display applications. To investigate and optimize the diffraction properties, we build a rigorous simulation model based on finite element method. To illustrate its potential applications, we propose a simple 2D/3D wearable display using a planar waveguide comprising of two reflective PVGs.
The role of iron in the growth of human leukemic cell lines (1984)

The growth requirements of three human leukemic cell lines (K 562, HEL, U937) have been studied in the absence of serum. For growth in serum-free medium, the cells require insulin, transferrin, and albumin. Two highly water-soluble iron salts, ferric ammonium citrate and ferric ammonium sulfate, may completely replace transferrin for supporting the growth of these cell lines. Similar results were obtained when mitogen-stimulated lymphocytes were grown in serum-free media. Iron containing compounds, such as hemin or hemoglobin, were also able to replace transferrin. Experiments using 42/6 monoclonal antibody strongly suggest that free-iron salts are taken up by the cells by a mechanism that is completely independent from transferrin-receptors.
Active site mutants of human cyclophilin A separate peptidyl‐prolyl isomerase activity from cyclosporin A binding and calcineurin inhibition (1992)

Based on recent X-ray structural information, six site-directed mutants of human cyclophilin A (hCyPA) involving residues in the putative active site--H54, R55, F60, Q111, F113, and H126--have been constructed, overexpressed, and purified from Escherichia coli to homogeneity. The proteins W121A (Liu, J., Chen, C.-M., & Walsh, C.T., 1991a, Biochemistry 30, 2306-2310), H54Q, R55A, F60A, Q111A, F113A, and H126Q were assayed for cis-trans peptidyl-prolyl isomerase (PPIase) activity, their ability to bind the immunosuppressive drug cyclosporin A (CsA), and protein phosphatase 2B (calcineurin) inhibition in the presence of CsA. Results indicate that H54Q, Q111A, F113A, and W121A retain 3-15% of the catalytic efficiency (kcat/Km) of wild-type recombinant hCyPA. The remaining three mutants (R55A, F60A, and H126Q) each retain less than 1% of the wild-type catalytic efficiency, indicating participation by these residues in PPIase catalysis. Each of the mutants bound to a CsA affinity matrix. The mutants R55A, F60A, F113A, and H126Q inhibited calcineurin in the presence of CsA, whereas W121A did not. Although CsA is a competitive inhibitor of PPIase activity, it can complex with enzymatically inactive cyclophilins and inhibit the phosphatase activity of calcineurin.
<title>Feedback control of the vacuum-assisted resin transfer molding (VARTM) process</title> (1999)

The Vacuum Assisted Resin Transfer Molding (VARTM) technique is a liquid-molding process that offers the potential to significantly reduce fabrication costs for large-scale composite structures. The VARTM workcell is used to evaluate control strategies and sensors such as SMARTweave to provide feedback for an intelligent control system. Current VARTM systems lack automated control systems resulting in part to part variability. This research presents a continuously controlled vacuum actuator system and the influence of vacuum gradients on resin flow front control.
Ectopic restriction of DNA repair reveals that UNG2 excises AID-induced uracils predominantly or exclusively during G1 phase (2012)

Immunoglobulin (Ig) affinity maturation requires the enzyme AID, which converts cytosines (C) in Ig genes into uracils (U). This alone produces C:G to T:A transition mutations. Processing of U:G base pairs via U N-glycosylase 2 (UNG2) or MutSα generates further point mutations, predominantly at G:C or A:T base pairs, respectively, but it is unclear why processing is mutagenic. We aimed to test whether the cell cycle phase of U processing determines fidelity. Accordingly, we ectopically restricted UNG2 activity in vivo to predefined cell cycle phases by fusing a UNG2 inhibitor peptide to cell cycle-regulated degradation motifs. We found that excision of AID-induced U by UNG2 occurs predominantly during G1 phase, inducing faithful repair, mutagenic processing, and class switching. Surprisingly, UNG2 does not appear to process U:G base pairs at all in Ig genes outside G1 phase.
Loss of heterozygosity analysis defines a critical region in chromosome 1p22 commonly deleted in human malignant mesothelioma. (1996)

Previous cytogenetic analysis has revealed frequent losses of chromosome 1p21-22 in human malignant mesothelioma, suggesting that the loss or inactivation of a tumor suppressor gene's) residing at this site may contribute to the tumorigenic conversion of mesothelial cells. To more precisely define the location of the target gene, primary tumor specimens and cell lines from 50 malignant mesotheliomas were examined for loss of heterozygosity using short tandem repeat polymorphism (STRP) markers. Nineteen STRP markers established by the Cooperative Human Linkage Center were selected for the initial screening of the entire short arm of chromosome 1. Thirty-seven cases (74%) showed allelic losses at least at one locus in 1p. Thirty-six of these cases showed losses of 1p21-22, including 23 with partial deletions involving this region. To obtain a higher resolution map of this region, another 13 STRP markers from the Genethon map were used to define the shortest region of overlapping deletions to a 4-cM segment flanked by the loci D1S435 and D1S236. The chromosomal location of the critically deleted region was confirmed to be within 1p22 by karyotypic and fluorescence in situ hybridization analyses.
Small Neuroscience: The Nanostructure of the Central Nervous System and Emerging Nanotechnology Applications (2005)

The design and application of bionanotechnologies aimed at the central nervous system (CNS) provide powerful new approaches for studying cell and molecular biology and physiology. Emerging clinically oriented bionanotechnologies are targeting CNS pathologies such as trauma or degenerative events. The successful and meaningful development of bionanotechnologies designed to interact with the CNS as research or clinical tools require an understanding of the relevant neurophysiology and neuropathology, an appreciation of the inherent nanoscale structure of the CNS, and an understanding of the relevant chemistry and materials science and engineering. This review gives an introduction to the structure and organization of the CNS starting at the organ level and working down in spatial scale to the cellular and molecular levels, with specific examples of biological nanoengineering in neural cells. This is followed by a discussion of some of the unique challenges and obstacles associated with developing bionanotechnologies aimed at the CNS, and a discussion of emerging nanotechnologies for neuroscience applications.
Speech Recognition: From the Laboratory to the Real World (1990)

The art and science of speech recognition research have advanced to the point where it is now possible to communicate reliably with a machine via telephone to carry out simple tasks. However, the creation of robust algorithms is only part of the overall process of making speech recognition technology a commercial reality. In this paper, we present a brief overview of speech recognition technology and discuss the implementation of the algorithms with digital signal processing chips. In addition, we will show how theory and practice come together in real-world conditions by describing a telephone network trial of automatic credit card verification using speech recognition technology.
Transformation of Acinetobacter sp. Strain BD413 by Transgenic Sugar Beet DNA (1998)

The ability of Acinetobacter sp. strain BD413(pFG4 delta nptII) to take up and integrate transgenic plant DNA based on homologous recombination was studied under optimized laboratory conditions. Restoration of nptII, resulting in kanamycin-resistant transformants, was observed with plasmid DNA, plant DNA, and homogenates carrying the gene nptII. Molecular analysis showed that some transformants not only restored the 317-bp deletion but also obtained additional DNA.
Controlled Gene Delivery by DNA–Gelatin Nanospheres (1998)

A novel system for gene delivery, based on the use of DNA-gelatin nanoparticles (nanospheres) formed by salt-induced complex coacervation of gelatin and plasmid DNA, has been developed. These particles were spherical, with a size range of 200-700 nm, contained 25-30% (w/w) DNA, and were stabilized by cross-linking of gelatin. As a consequence of being controlled by the cross-linking density of the gelatin matrix, the average release rate of DNA from nanospheres synthesized under standard conditions was 2.2%/day in serum. Nanosphere DNA incubated in bovine serum was more resistant to nuclease digestion than was naked DNA. Various bioactive agents could be encapsulated in the nanospheres by ionic interaction with the matrix components, physical entrapment, or covalent conjugation. Transfection of cultured cells with a luciferase plasmid was enhanced by conjugating human transferrin onto the nanosphere and coencapsulating the endolysolytic agent chloroquine. Under our experimental conditions, gene expression in mice subsequent to intramuscular injection of nanospheres containing 1 microg of a beta-galactosidase plasmid was greater and more prolonged than was observed after injection of an equal amount of naked DNA or DNA complexed with Lipofectamine.
Sizes and concentrations of several type C oncornaviruses and bacteriophage T2 by the resistive-pulse technique (1977)

Viruses above about 60 nm in diameter may be rapidly sized to a few nanometers in their natural hydrated state as they pass one by one through a single pore in a newly developed nanometer-particle analyzer based on the resistive-pulse technique of the Coulter Counter and the use of submicron diameter pores made by the Nuclepore process. Size measurements for several type C oncornaviruses are: Rauscher murine leukemia, 122.3 +/- 2 nm; simian sarcoma, 109.7 +/- 3 nm; Mason-Pfizer monkey, 140.0 +/- 2.5 nm; RD-114, 115 +/- 5 nm; and feline leukemia, 127.4 +/- 2 nm, relative to standard 109-nm latex spheres. The T2 bacteriophage has a volume of (5.10 +/- 0.15) X 10(-16) cm3. Concentrations of viruses near 10(9) to 10(11)/ml that are fairly clear of debris are routinely measurable in a few minutes to an accuracy near 15%. A lower practical count limit is near 5 X 10(7) viruses per ml.
Wave similarity of human ventricular fibrillation from bipolar electrograms (2007)

Wave similarity analysis provides a tool for assessing directional organization in human VF. This analysis of directional organization may have implications for the study of mechanisms of VF in the clinical arena.
Hydroxyrubicin, a deaminated derivative of doxorubicin, inhibits mammalian DNA topoisomerase II and partially circumvents multidrug resistance (1994)

In vivo effectiveness of doxorubicin remains restricted due to toxicity and drug resistance. Hydroxyrubicin is a synthetic analog of doxorubicin in which the basic amino group at the C-3' has been replaced by a hydroxyl group in order to overcome recognition by the multidrug resistant (MDR) P-glycoprotein and limit cardiotoxicity. The present study shows that hydroxyrubicin is a less potent intercalator than doxorubicin. Induction of topoisomerase II-mediated DNA cleavage in the human c-myc origin by the two drugs was similar, reaching a maximum at 0.5 microM. Results from the NCI Cell Screening program indicate a relatively good correlation between the cytotoxicity of the 2 drugs on 55 cell lines of various origins (r = 0.723). Using a clonogenic assay, we observed that hydroxyrubicin was 20-fold more cytotoxic against the MDR KB-V1 cell line than doxorubicin and was slightly more cytotoxic than doxorubicin in the sensitive KB3.1 cell line. Uptake studies showed that doxorubicin was retained up to 1 hr in KB3.1 cells and rapidly eliminated from resistant KB-V1 cells. In contrast, hydroxyrubicin was rapidly eliminated from both sensitive KB3.1 and MDR-positive KB-V1 cells. Both drugs induced protein-linked DNA single-strand breaks (SSBs) in both KB3.1 and KB-V1 cells, which is consistent with topoisomerase inhibition. However, the kinetics of DNA SSBs induced by both drugs was very different. DNA breaks disappeared quickly in both KB3.1 and KB-V1 cell lines after hydroxyrubicin removal while DNA breaks induced by doxorubicin disappeared very slowly in KB3.1 cells and rapidly in KB-V1 cells. We conclude that removal of the basic amino group at the C-3' of doxorubicin modifies drug transport and partially circumvents MDR without changing topoisomerase II inhibition when compared with doxorubicin.
Antiestrogenic Effect of R5020, a Synthetic Progestin in Human Breast Cancer Cells in Culture* (1983)

To see whether progestins prevent estrogen action in breast cancer cells, we have studied in vitro the effect of R5020 on the cell growth and the synthesis of secreted proteins in T47D and R27 human breast cancer cells. While R5020 had no effect on cell growth when tested alone, it significantly inhibited the growth of both cell lines in the presence of estradiol (1 nM). The effect was most clear-cut after 10-12 days of treatment and was dose dependent, a half-maximal inhibition occurred with 1 nM R5020. R27, a cloned MCF7 variant resistant to Tamoxifen, remained responsive to R5020, which prevented the effect of 17 beta-estradiol (E2) and inhibited cell growth in the presence of Tamoxifen. This suggests that the two antiestrogens are acting through different mechanisms. Dihydrotestosterone and dexamethasone did not reproduce or inhibit the effect of R5020 on cell growth. R5020 was ineffective in a rat tumor cell line containing androgen and glucocorticoid receptors but lacking progesterone receptors and estrogen receptors. These results suggest that R5020 is probably acting via progesterone receptors rather than via the androgen or glucocorticoid receptors. Using sodium dodecyl sulfate-polyacrylamide gel electrophoresis, we have shown that R5020 specifically decreases the production of the 52K protein, a major protein released by R27 cells after E2 stimulation. We conclude that R5020 has an antiestrogenic activity on breast cancer cells in culture, since it prevents the stimulation of cell growth and protein synthesis by E2.
Bacterial Probiotics Induce an Immune Response in the Honey Bee (Hymenoptera: Apidae) (2004)

To explore immune system activation in the honey bee, Apis mellifera L., larvae of four ages were exposed through feeding to spores of a natural pathogen, Paenibacillus larvae larvae, to cells of a diverse set of related nonpathogenic bacteria, and to bacterial coat components. These larvae were then assayed for RNA levels of genes encoding two antibacterial peptides, abaecin and defensin. Larvae exposed to either P. l. larvae or a mix of nonpathogenic bacteria showed high RNA levels for the abaecin gene relative to controls. First instars responded significantly to the presence of the nonpathogenic mix within 12 h after exposure, a time when they remain highly susceptible to bacterial invasion. This response was sustained for two successive instars, eventually becoming 21-fold higher in larvae exposed to probiotic spores versus control larvae. The mixture of nonpathogenic bacteria is therefore presented as a potential surrogate for assaying the immune responses of different honey bee lineages. It also is proposed that nonpathogenic bacteria can be used as a probiotic to enhance honey bee immunity, helping bee larvae, and other life stages, survive attacks from pathogens in the field.
Identification of a Small Subpopulation of Candidate Leukemia-Initiating Cells in the Side Population of Patients with Acute Myeloid Leukemia (2008)

In acute myeloid leukemia (AML), apart from the CD34(+)CD38(-) compartment, the side population (SP) compartment contains leukemic stem cells (LSCs). We have previously shown that CD34(+)CD38(-) LSCs can be identified using stem cell-associated cell surface markers, including C-type lectin-like molecule-1 (CLL-1), and lineage markers, such as CD7, CD19, and CD56. A similar study was performed for AML SP to further characterize the SP cells with the aim of narrowing down the putatively very low stem cell fraction. Fluorescence-activated cell sorting (FACS) analysis of 48 bone marrow and peripheral blood samples at diagnosis showed SP cells in 41 of 48 cases that were partly or completely positive for the markers, including CD123. SP cells in normal bone marrow (NBM) were completely negative for markers, except CD123. Further analysis revealed that the SP fraction contains different subpopulations: (a) three small lymphoid subpopulations (with T-, B-, or natural killer-cell markers); (b) a differentiated myeloid population with high forward scatter (FSC(high)) and high sideward scatter (SSC(high)), high CD38 expression, and usually with aberrant marker expression; (c) a more primitive FSC(low)/SSC(low), CD38(low), marker-negative myeloid fraction; and (d) a more primitive FSC(low)/SSC(low), CD38(low), marker-positive myeloid fraction. NBM contained the first three populations, although the aberrant markers were absent in the second population. Suspension culture assay showed that FSC(low)/SSC(low) SP cells were highly enriched for primitive cells. Fluorescence in situ hybridization (FISH) analyses showed that cytogenetically abnormal colonies originated from sorted marker positive cells, whereas the cytogenetically normal colonies originated from sorted marker-negative cells. In conclusion, AML SP cells could be discriminated from normal SP cells at diagnosis on the basis of expression of CLL-1 and lineage markers. This reveals the presence of a low-frequency (median, 0.0016%) SP subfraction as a likely candidate to be enriched for leukemia stem cells.
An obstacle-edging reflex for an autonomous lawnmower (2010)

We developed a controller that allows our prototype lawnmower, CWRU Cutter, 1st place winner of the 2009 ION Autonomous Lawnmower Competition, to follow pre-defined paths and reflexively edge around obstacles before returning to the path. CWRU Cutter is equipped with localization sensors (GPS) and obstacle detecting sensors (LIDAR and camera).
Cytotoxicity of chimeric (human-murine) monoclonal antibody BR96 IgG, F(ab')2, and Fab' conjugated to Pseudomonas exotoxin (1992)

We have made antigen-specific cytotoxic reagents by conjugating the chimeric antibody BR96 (chiBR96) to Pseudomonas exotoxin A (PE), as either native PE or a truncated form (LysPE40) devoid of the cell-recognition region (domain I). PE kills cells by ADP-ribosylation of elongation factor 2, thereby inhibiting protein synthesis. Chimeric BR96 immunotoxins were constructed by chemical conjugation of the toxin to Fab', F(ab')2, and intact IgG and purified by anion-exchange and gel-filtration chromatography. Chimeric BR96 [IgG and F(ab')2] immunotoxins were cytotoxic against tumor cell lines displaying the BR96 antigen, with EC50 values ranging from 0.1 to 110 pM. Immunotoxins constructed with chiBR96 Fab' were 50-100-fold less cytotoxic. Competition analysis showed that the immunotoxins were specifically active through their BR96 antigen-binding ability. The binding of chiBR96-PE and chiBR96-LysPE40 to antigen was equivalent to that of BR96 itself and these immunotoxins were found to internalize very rapidly, displaying 90% of their cytotoxicity within 1 h. Binding assays determined that chiBR96 F(ab')2-LysPE40 bound as well as chiBR96-LysPE40; however, chiBR96 Fab'-LysPE40 bound 20-fold less efficiently. The chiBR96 Fab'-LysPE40 internalized similarly to the F(ab')2 or the IgG immunotoxins. Therefore, the chiBR96 Fab'-LysPE40 immunotoxin is less cytotoxic toward target cells because of reduced antigen binding. This is may be due to the monovalent nature of chiBR96 Fab'-LysPE40. This study shows that the monoclonal antibody chiBR96-Pseudomonas exotoxin A immunotoxins can be effective at inhibiting protein synthesis in target cells.
A Review of T‐Cell Receptors in Multiple Sclerosis: Clonal Expansion and Persistence of Human T‐Cells Specific for an Immunodominant Myelin Basic Protein Peptidea (1995)

Understanding the immune response to myelin antigens in regard to the peptide/MHC/TCR complex is important in defining pathogenesis of demyelinating autoimmune diseases and in developing antigen-specific therapies. We previously reported that individual multiple sclerosis patients may use certain dominant TCR V beta chains to recognize immunodominant MBP peptides. In examining the TCR beta chain usage, we observed repeated TCR VDJ sequences among different T-cell lines isolated from the same patient. This suggested that a few expanded T-cell clones may dominate the immune response to immunodominant MBP peptides. Here, we report experiments where TCR rearrangements were used as a probe for the clonal origin of MBP specific T-cells cultured from blood lymphocytes of MS patients and normal subjects. In two patients with the DR2 haplotype that were analyzed in detail, the T-cell response to MBP was focused on the MBP (84-102) peptide and in vivo expanded population(s) dominated the response to the MBP (84-102) peptide. Two MBP (84-102) specific T-cell clones from a normal subject with the DR2 haplotype were also found to have identical TCR sequences. Clonality was proven by demonstrating that independent clones had identical TCR alpha and beta chain sequences as well as identical sequences of a TCR gamma chain or of a second TCR alpha chain rearrangement. These data suggest that the response to human MBP is dominated in at least some subjects by expanded clones that may persist in vivo for relatively long periods of time.