gebhart/patrepeval huggingface dataset:
Personalized interactive faceted search (2008)

Faceted search is becoming a popular method to allow users to interactively search and navigate complex information spaces. A faceted search system presents users with key-value metadata that is used for query refinement. While popular in e-commerce and digital libraries, not much research has been conducted on which metadata to present to a user in order to improve the search experience. Nor are there repeatable benchmarks for evaluating a faceted search engine. This paper proposes the use of collaborative filtering and personalization to customize the search interface to each user's behavior. This paper also proposes a utility based framework to evaluate the faceted interface. In order to demonstrate these ideas and better understand personalized faceted search, several faceted search algorithms are proposed and evaluated using the novel evaluation methodology.
Amniotic Fluid-Derived Mesenchymal Stem Cells Prevent Fibrosis and Preserve Renal Function in a Preclinical Porcine Model of Kidney Transplantation (2014)

It is well known that ischemia/reperfusion injuries strongly affect the success of human organ transplantation. Development of interstitial fibrosis and tubular atrophy is the main deleterious phenomenon involved. Stem cells are a promising therapeutic tool already validated in various ischemic diseases. Amniotic fluid-derived mesenchymal stem cells (af-MSCs), a subpopulation of multipotent cells identified in amniotic fluid, are known to secrete growth factors and anti-inflammatory cytokines. In addition, these cells are easy to collect, present higher proliferation and self-renewal rates compared with other adult stem cells (ASCs), and are suitable for banking. Consequently, af-MSCs represent a promising source of stem cells for regenerative therapies in humans. To determine the efficiency and the safety of af-MSC infusion in a preclinical porcine model of renal autotransplantation, we injected autologous af-MSCs in the renal artery 6 days after transplantation. The af-MSC injection improved glomerular and tubular functions, leading to full renal function recovery and abrogated fibrosis development at 3 months. The strong proof of concept generated by this translational porcine model is a first step toward evaluation of af-MSC-based therapies in human kidney transplantation.
Transfer of extracellular vesicles during immune cell‐cell interactions (2012)

The transfer of molecules between cells during cognate immune cell interactions has been reported, and recently a novel mechanism of transfer of proteins and genetic material such as small RNA between T cells and antigen-presenting cells (APCs) has been described, involving exchange of extracellular vesicles (EVs) during the formation of the immunological synapse (IS). EVs, a term that encompasses exosomes and microvesicles, has been implicated in cell-cell communication during immune responses associated with tumors, pathogens, allergies, and autoimmune diseases. This review focuses on EV transfer as a mechanism for the exchange of molecules during immune cell-cell interactions.
The Application of Area-Reconstruction Operator in Automatic Visual Inspection of Quality Control (2006)

In order to detect the impurities on the surface of orange segment, a PC-based automatic real-time visual inspection system was designed. First a new connected operator named Area-reconstruction operator for binary image was introduced, which could filter connected components according to mask image, marker image and area of corresponding region. Then the application of Area-reconstruction operator to perform segmentation of orange image was presented, where mask image and marker image were formed by region growing and region reducing. Operation parameters of image-processing were obtained by genetic algorithm on train mode. Experimental result indicates that only the proposed image processing method may get the satisfactory result and the on-line implementation ability of the inspection system is about 30∼40 segments per second with adequate accuracy.
Three-Dimensional Integrated Circuit Layout (1991)

First published in 1991, this thesis concentrates upon the design of three-dimensional, rather than the traditional two-dimensional, circuits. The theory behind such circuits is presented in detail, together with experimental results. Winner of the Distinguished Dissertation in Computer Science award, this work will prove invaluable to both designers and hardware engineers involved in the development of practical three-dimensional integrated circuits.
Computer Program to Assist in Making Decisions About Adjuvant Therapy for Women With Early Breast Cancer (2001)

The computer program Adjuvant! can play practical and educational roles in clinical settings.
<title>Compact HMD optics based on multiplexed aberration-compensated holographic optical elements</title> (2001)

Head and helmet mounted displays (HMDs) can benefit greatly from new wide field-of-view, compact visor optics to project very high resolution (e.g., 5k X 4k) imagery. Physical Optics Corporation (POC) is developing novel, compact, lightweight wide field-of-view optics based on three-color multiplexed aberration-compensated holographic optical elements (MAC-HOEs). Taking advantage of the flexibility of holography, the HMD optics can be made compact using waveguide projection through the curved visor substrate, so that the see-through visor can have a wide field-of-view without large, bulky optical components. Using narrowband red-green-blue hologram multiplexing, MAC-HOEs can significantly reduce the chromatic and geometrical aberration introduced by conventional HOEs and refractive optics. In the initial phase of development, POC demonstrated the feasibility of the HMD optics through computer design and analysis, and by fabricating and demonstrating a MAC-HOE component.
A multi-epitope vaccine based on &lt;italic&gt;Chlamydia trachomatis&lt;/italic&gt; major outer membrane protein induces specific immunity in mice (2014)

We evaluated the immunogenicity and efficacy of a candidate vaccine comprising the major outer membrane protein (MOMP) multi-epitope of Chlamydia trachomatis. A short gene of multi-epitope derived from MOMP containing multiple T- and B-cell epitopes was artificially synthesized. The recombinant plasmid pET32a(+) containing codon optimized MOMP multi-epitope gene was constructed. Expression of the fusion protein Trx-His-MOMP multi-epitope in Escherichia coli was confirmed by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and western blot analysis. Balb/c mice were inoculated with the purified fusion protein subcutaneously three times with 2-week intervals. Results showed that the MOMP multi-epitope elicited not only strong humoral immune responses to C. trachomatis by generating significantly high levels of specific antibodies (IgG1 and IgG2a), but also a cellular immune response by inducing robust cytotoxic T lymphocyte responses in mice. Furthermore, the MOMP multi-epitope substantially primed secretion of IFN-γ, revealing that this vaccine could induce a strong Th1 response. Finally, the mice vaccinated with the MOMP multi-epitope displayed a reduction of C. trachomatis shedding upon a chlamydial challenge and an accelerated clearance of the infected C. trachomatis. In conclusion, the MOMP multi-epitope vaccine may have the potentiality for the development of effective prophylactic and therapeutic vaccines against the C. trachomatis infection.
Receptor Tyrosine Kinases and Targeted Cancer Therapeutics (2011)

The majority of growth factor receptors are composed of extracellular, transmembrane, and cytoplasmic tyrosine kinase (TK) domains. Receptor tyrosine kinase (RTK) activation regulates many key processes including cell growth and survival. However, dysregulation of RTK has been found in a wide range of cancers, and it has been shown to correlate with the development and progression of numerous cancers. Therefore, RTK has become an attractive therapeutic target. One way to effectively block signaling from RTK is inhibition of its catalytic activity with small-molecule inhibitors. Low-molecular-weight TK inhibitors (TKIs), such as imatinib, targeting tumors with mutant c-Kit, and gefitinib, targeting non-small cell lung cancer with mutant epidermal growth factor receptor (EGFR), have received marketing approval in Japan. MET, fibroblast growth factor receptor (FGFR), and insulin-like growth factor-I receptor (IGF-IR) are frequently genetically altered in advanced cancers. TKIs of these receptors have not yet appeared on the market, but many anticancer drug candidates are currently undergoing clinical trials. Most of these TKIs were designed to compete with ATP at the ATP-binding site within the TK domain. This review will focus on small-molecule TKIs targeting MET, FGFR, and IGF-IR and discuss the merits and demerits of two types of agents, i.e., those with only one or a few targets and those directed at multiple targets. Targeting agents specifically inhibiting the target kinase were previously searched for based on the hypothesis that a narrow target window might reduce unexpected side effects, but agents with multiple targets have been recently developed to overcome tumors resistant against a single-targeting agent.
LsbB Bacteriocin Interacts with the Third Transmembrane Domain of the YvjB Receptor (2016)

The Zn-dependent membrane-located protease YvjB has previously been shown to serve as a target receptor for LsbB, a class II leaderless lactococcal bacteriocin. Although yvjB is highly conserved in the genus Lactococcus, the bacteriocin appears to be active only against the subspecies L. lactis subsp. lactis Comparative analysis of the YvjB proteins of a sensitive strain (YvjBMN) and a resistant strain (YvjBMG) showed that they differ from each other in 31 positions. In this study, we applied site-directed mutagenesis and performed directed binding studies to provide biochemical evidence that LsbB interacts with the third transmembrane helix of YvjB in susceptible cells. The site-directed mutagenesis of LsbB and YvjB proteins showed that certain amino acids and the length of LsbB are responsible for the bacteriocin activity, most probably through adequate interaction of these two proteins; the essential amino acids in LsbB responsible for the activity are tryptophan (Trp(25)) and terminal alanine (Ala(30)). It was also shown that the distance between Trp(25) and terminal alanine is crucial for LsbB activity. The crucial region in YvjB for the interaction with LsbB is the beginning of the third transmembrane helix, particularly amino acids tyrosine (Tyr(356)) and alanine (Ala(353)). In vitro experiments showed that LsbB could interact with both YvjBMN and YvjBMG, but the strength of interaction is significantly less with YvjBMG In vivo experiments with immunofluorescently labeled antibody demonstrated that LsbB specifically interacts only with cells carrying YvjBMN IMPORTANCE: The antimicrobial activity of LsbB bacteriocin depends on the correct interaction with the corresponding receptor in the bacterial membrane of sensitive cells. Membrane-located bacteriocin receptors have essential primary functions, such as cell wall synthesis or sugar transport, and it seems that interaction with bacteriocins is suicidal for cells. This study showed that the C-terminal part of LsbB is crucial for the bacteriocin activity, most probably through adequate interaction with the third transmembrane domain of the YvjB receptor. The conserved Tyr(356) and Ala(353) residues of YvjB are essential for the function of this Zn-dependent membrane-located protease as a bacteriocin receptor.
A&#946;(1-42) Aggregates into Non-Toxic Amyloid Assemblies in the Presence of the Natural Polyphenol Oleuropein Aglycon (2011)

Amyloid aggregation starts with the initial misfolding of peptide/protein precursors, with subsequent structural rearrangement into oligomers and protofibrils; the latter eventually organize into fibrils with shared basic structural features, found deposited in amyloid diseases. Mounting evidence indicates early oligomers as the most toxic amyloid species; accordingly, the search of inhibitors of their growth is considered a promising target to prevent amyloid toxicity. We recently showed that oleuropein aglycon, a polyphenol abundant in the extra virgin olive oil, interferes with the aggregation of amylin (involved in type-2 diabetes), eliminating its cytotoxicity. Here we report that oleuropein aglycon also hinders amyloid aggregation of Aβ(1-42) and its cytotoxicity, suggesting a general effect of such polyphenol. In particular, by using a wide panel of different spectroscopic, immunologic, cell viability and imaging techniques we provide a more detailed description of Aβ(1-42) structural modifications arising in the presence of the inhibitor and the resulting cytotoxicity. We here report that the polyphenol eliminates the appearance of early toxic oligomers favouring the formation of stable harmless protofibrils, structurally different from the typical Aβ(1-42) fibrils. We also show that oleuropein aglycon is maximally effective when is present at the beginning of the aggregation process; furthermore, when added to preformed fibrils, it does not induce the release of toxic oligomers but, rather, neutralizes any residual toxicity possibly arising from the residual presence of traces of soluble oligomers and other toxic aggregates. The possible use of this polyphenol as anti-aggregation molecule is discussed in the light of these data.
Recent Development in ITO-free Flexible Polymer Solar Cells (2017)

Polymer solar cells have shown good prospect for development due to their advantages of low-cost, light-weight, solution processable fabrication, and mechanical flexibility. Their compatibility with the industrial roll-to-roll manufacturing process makes it superior to other kind of solar cells. Normally, indium tin oxide (ITO) is adopted as the transparent electrode in polymer solar cells, which combines good conductivity and transparency. However, some intrinsic weaknesses of ITO restrict its large scale applications in the future, including a high fabrication price using high temperature vacuum deposition method, scarcity of indium, brittleness and scaling up of resistance with the increase of area. Some substitutes to ITO have emerged in recent years, which can be used in flexible polymer solar cells. This article provides the review on recent progress using other transparent electrodes, including carbon nanotubes, graphene, metal nanowires and nanogrids, conductive polymer, and some other electrodes. Device stability is also discussed briefly.
Nomenclature for factors of the HLA system, update May 2009 (2009)

The following sequences have been submitted to the Nomenclature Committee since the April 2009 nomenclature update and, following agreed policy, have been assigned official allele designations. Full details of all sequences will be published in a forthcoming report. Below are listed the newly assigned sequences (Table 1) and confirmations of previously reported sequences (Table 2). The accession number of each sequence is given and these can be used to retrieve the sequence files from the EMBL, GenBank, Vega or DDBJ data libraries. Although accession numbers have been assigned by the data-libraries and most sequences are already available, there is still the possibility that an author may not yet have allowed the sequence to be released; in such a case you will have to contact the submitting author directly. Additional information pertaining to new sequences is often included in the publications describing these alleles; a listing of recent publications that describe new HLA sequences is given in Table 3. All new and confirmatory sequences should now be submitted directly to the WHO Nomenclature Committee for Factors of the HLA System via the IMGT/HLA Database using the sequence submission tool provided. The IMGT/HLA Database may be accessed via the World Wide Web at: www.ebi.ac.uk/imgt/hla
Practical minimal perfect hash functions for large databases (1992)

article Free Access Share on Practical minimal perfect hash functions for large databases Authors: Edward A. Fox Virginia Polytechnic Institute and State Univ., Blacksburg, VA Virginia Polytechnic Institute and State Univ., Blacksburg, VAView Profile , Lenwood S. Heath Virginia Polytechnic Institute and State Univ., Blacksburg, VA Virginia Polytechnic Institute and State Univ., Blacksburg, VAView Profile , Qi Fan Chen Virginia Polytechnic Institute and State Univ., Blacksburg, VA Virginia Polytechnic Institute and State Univ., Blacksburg, VAView Profile , Amjad M. Daoud Western Geophysical, Houston, TX Western Geophysical, Houston, TXView Profile Authors Info & Claims Communications of the ACMVolume 35Issue 1Jan. 1992 pp 105–121https://doi.org/10.1145/129617.129623Published:02 January 1992Publication History 71citation2,057DownloadsMetricsTotal Citations71Total Downloads2,057Last 12 Months67Last 6 weeks12 Get Citation AlertsNew Citation Alert added!This alert has been successfully added and will be sent to:You will be notified whenever a record that you have chosen has been cited.To manage your alert preferences, click on the button below.Manage my Alerts New Citation Alert!Please log in to your account Save to BinderSave to BinderCreate a New BinderNameCancelCreateExport CitationPublisher SiteeReaderPDF
Selection of T cell receptor variable gene‐encoded amino acids on the third binding site loop: a factor influencing variable chain selection in a T cell response (1995)

The 3' end of the T cell receptor V beta 7.1 gene contains the five nucleotides CAAGA between the broadly conserved consensus sequence of nucleotides TGC/T GCC AGC AGC (which encode cysteine, alanine, serine and serine at positions 92-95 of the beta chain) and the heptamer that signals rearrangement. These nucleotides are frequently preserved during gene rearrangement, resulting in the common presence of glutamine at position 96 and of aspartate or glutamate at position 97 of the V beta 7.1 chain CDR3 loop in peripheral blood lymphocytes. There is selection of V beta 7.1 and of the V beta 7.1 gene-encoded glutamate at position 97 of the beta chain CDR3 loop in the cytotoxic T lymphocyte response to the HLA B2705-restricted influenza A nucleoprotein epitope SRYWAIRTR. Our results indicate that selection of V beta 7.1 gene-encoded amino acid residues on CDR3 loops may be one factor driving selection of V beta 7.1 in this response.
Decrease in mitochondrial energy coupling by thyroid hormones: a physiological effect rather than a pathological hyperthyroidism consequence (1998)

The effect of the in vivo thyroid status on mitochondrial membrane potential (delta psi(m)) in isolated rat hepatocytes was studies by means of a cytofluorimetric technique and the delta psi(m)-specific probe JC-1. It is shown that the delta psi(m) level decreases in the order hypothyroid > euthyroid > hyperthyroid. Polarographic measurement of the hepatocyte respiratory rates revealed an opposite trend of values: the highest respiratory rate in hepatocytes from hyperthyroid animals, the lowest in those from hypothyroid ones. This means that mitochondrial energy coupling is highest in hypothyroid hepatocytes and lowest in hyperthyroid hepatocytes. 6-Ketocholestanol added to hepatocytes failed to counterbalance the uncoupling effect of thyroid hormones on delta psi(m) and respiration rate. Under the same conditions, 6-ketocholestanol appeared to be effective in recoupling of respiration uncoupled by low concentrations of the artificial protonophore FCCP. The mechanism and possible physiological functions of the thyroid hormone-induced decrease in mitochondrial energy coupling are discussed.
The multiple alterations of Heparan sulphate in cancer (2013)

Introduction Heparan sulphate is a complex polysaccharide that contains specific structural patterns generated through a series of interdependent enzymatic reactions that can involve various isoenzymes with differences in their specificities, responsible for the modification of the structure of heparan sulphate in physiological and pathological processes. The aim of this review is to discuss the multiple alterations of heparan sulphate in cancer. Discussion Tumour cells exhibit altered growth patterns and metabolism. This is supported by deregulated expression of multiple gene sets associated with tumour development and progression. Malignant cancers are characterized by their invasiveness and can even metastasize to distant locations in the body. Heparan sulphate proteoglycans are implicated in these processes and can influence the growth, invasion and metastatic properties of cancerous cells. Cells exercise exquisite control over heparan sulphate composition and sequence, varying among cell types, development stages as a result of cell transformation in pathological processes. Numerous tumours show quantitative and structural alterations of heparan sulphate chains, largely caused by changes in the expression of the enzymes responsible for their biosynthesis, particularly at the fine structure level. Conclusion This article focuses on reviewing the type of changes that occur at different stages of heparan sulphate chain biosynthesis in various tumours. Altered transcription can occur in any phase of heparan sulphate biosynthesis, but is particularly frequent at the level of the family of the 3-O-sulphotransferases, and the families of the 6-Osulphotransferases and extracellular sulphatases. The result is the alteration of the ligand binding sites responsible for directing specific cell signalling effects, facilitating tumour progression.
On the Optimality of Single-Carrier Transmission in Large-Scale Antenna Systems (2012)

A single carrier transmission scheme is presented for the frequency selective multi-user (MU) multiple-input single-output (MISO) Gaussian Broadcast Channel (GBC) with a base station (BS) having M antennas and K single antenna users. The proposed transmission scheme has low complexity and for M ≥ K it is shown to achieve near optimal sum-rate performance at low transmit power to receiver noise power ratio. Additionally, the proposed transmission scheme results in an equalization-free receiver and does not require any MU resource allocation and associated control signaling overhead. Also, the sum-rate achieved by the proposed transmission scheme is shown to be independent of the channel power delay profile (PDP). In terms of power efficiency, the proposed transmission scheme also exhibits an O(M) array power gain. Simulations are used to confirm analytical observations.
Sphingolipid-modulated Exosome Secretion Promotes Clearance of Amyloid-β by Microglia (2012)

Amyloid β-peptide (Aβ), the pathogenic agent of Alzheimer disease, is a physiological metabolite whose levels are constantly controlled in normal brain. Recent studies have demonstrated that a fraction of extracellular Aβ is associated with exosomes, small membrane vesicles of endosomal origin, although the fate of Aβ in association with exosome is largely unknown. In this study, we identified novel roles for neuron-derived exosomes acting on extracellular Aβ, i.e. exosomes drive conformational changes in Aβ to form nontoxic amyloid fibrils and promote uptake of Aβ by microglia. The Aβ internalized together with exosomes was further transported to lysosomes and degraded. We also found that blockade of phosphatidylserine on the surface of exosomes by annexin V not only prevented exosome uptake but also suppressed Aβ incorporation into microglia. In addition, we demonstrated that secretion of neuron-derived exosomes was modulated by the activities of sphingolipid-metabolizing enzymes, including neutral sphingomyelinase 2 (nSMase2) and sphingomyelin synthase 2 (SMS2). In transwell experiments, up-regulation of exosome secretion from neuronal cells by treatment with SMS2 siRNA enhanced Aβ uptake into microglial cells and significantly decreased extracellular levels of Aβ. Our findings indicate a novel mechanism responsible for clearance of Aβ through its association with exosomes. The modulation of the vesicle release and/or elimination may alter the risk of AD.