gebhart/patrepeval huggingface dataset:
Flavonolignan and Flavone Inhibitors of a Staphylococcus aureus Multidrug Resistance Pump:  Structure−Activity Relationships (2000)

Although some progress has been reported on structure-activity relationships (SARs) for inhibitors of mammalian P-glycoprotein MDR efflux pumps, there is almost nothing in the literature regarding SARs for inhibitors of any bacterial efflux pump. Indeed, only a few of these have been described. Our discovery of a potent naturally occurring flavonolignan inhibitor of the NorA MDR pump of Staphylococcus aureus provided a structural foundation upon which SARs could be assessed via synthetic analogues. Several flavonolignans were prepared which proved to have greater potency than the natural isolate, 5'-methoxyhydnocarpin-D, while others showed decreased potency. Surprisingly, some simple alkylated flavones also were quite active MDR pump inhibitors. Variability of activity among the compounds tested was sufficient so that at least some SARs could be postulated and compared with those known for P-glycoprotein.
Oral Candida: Clearance, Colonization, or Candidiasis? (1995)

Candida albicans is frequently isolated from the human mouth, yet few carriers develop clinical signs of candidiasis. Oral candidiasis presents clinically in many forms. This reflects the ability of the yeast to colonize different oral surfaces and the variety of factors which predispose the host to Candida colonization and subsequent infection. Colonization of the oral cavity appears to be facilitated by several specific adherence interactions between C. albicans and oral surfaces which enable the yeast to resist host clearance mechanisms. Thus, Candida has been shown to adhere to complement receptors, various extracellular matrix proteins, and specific sugar residues displayed on host or bacterial surfaces in the oral cavity. Oral candidiasis results from yeast overgrowth and penetration of the oral tissues when the host's physical and immunological defenses have been undermined. Tissue invasion may be assisted by secreted hydrolytic enzymes, hyphal formation, and contact sensing. While these and other phenotypic characteristics may endow certain Candida species or strains with a competitive advantage in the oral cavity, it is the host's immune competence that ultimately determines whether clearance, colonization, or candidiasis occurs.
Systemic Gene Therapy with p53 Reduces Growth and Metastases of a Malignant Human Breast Cancer in Nude Mice (1995)

We report on an in vivo delivery system that attenuates the growth, in nude mice, of a malignant human breast cancer cell line containing a p53 mutation. Nude mice, inoculated with breast carcinoma cells, were injected every 10-12 days with a liposome-p53 complex via the tail vein. A significant reduction of greater than 60% in primary tumor volume was observed as compared to the control groups. Furthermore, when individual growth patterns of the tumors were assessed, we found that primary tumor size regressed in the majority of p53-treated animals (8/15), whereas only one tumor in the control groups (1/22) regressed. The eight tumors that regressed with the liposome-p53 complex showed no evidence of relapse for 1 month after the cessation of treatment. We also determined that the administration of the liposome-p53 complex reduced the incidence of metastases. The MDA-MB-435 tumor cells, transduced with the lacZ gene, facilitated quantitation of beta-galactosidase activity and tumor burden in the lungs. The number of metastatic cells in the lung was significantly lower in the p53-treated group (0.53 +/- 0.43 x 10(6), p < 0.01) than in either the vector-treated (8.1 +/- 3.7 x 10(6)) or untreated control groups (15.8 +/- 5.9 x 10(6)). Thus, systemic administration of the liposome-p53 complex reduced not only the size of the primary tumors but, more importantly, prevented the relapse and metastases of these tumors.
Characterization of IL-10-Secreting T Cells Derived from Regulatory CD4+CD25+ Cells by the TIRC7 Surface Marker (2008)

Natural CD25(+)CD4(+) regulatory T cells (Treg) are essential for self-tolerance and for the control of T cell-mediated immune pathologies. However, the identification of Tregs in an ongoing immune response or in inflamed tissues remains elusive. Our experiments indicate that TIRC7, T cell immune response cDNA 7, a novel membrane molecule involved in the regulation of T lymphocyte activation, identifies two Treg subsets (CD25(low)TIRC7(+) and CD25(high)TIRC7(-)) that are characterized by the expression of Foxp3 and a suppressive activity in vitro and in vivo. We also showed that the CD25(low)TIRC7(+) subset represents IL-10-secreting Tregs in steady state, which is accumulated intratumorally in a tumor-bearing mice model. Blockade of the effect of IL-10 reversed the suppression imposed by the CD25(low)TIRC7(+) subset. Interestingly, these IL-10-secreting cells derived from the CD25(high)TIRC7(-) subset, both in vitro and in vivo, in response to tumoral Ags. Our present results strongly support the notion that, in the pool of natural Tregs, some cells can recognize foreign Ags and that this recognition is an essential step in their expansion and suppressive activity in vivo.
Diffusion of adsorbates on metal surfaces (1990)

The theory of diffusion and the principal methods of determining surface diffusion coefficients are presented and their strengths and weaknesses discussed. A summary of major experimental results for diffusion of metallic and non-metallic adsorbates on metal surfaces is given and areas of agreement and disagreement between various measurements are discussed. A brief overview of principal conclusions, problem areas and future directions concludes the review.
Phase I Trial of Sorafenib and Gemcitabine in Advanced Solid Tumors with an Expanded Cohort in Advanced Pancreatic Cancer (2006)

Sorafenib and gemcitabine are well tolerated in combination; further evaluations in pancreatic and ovarian cancers are warranted.
A Game Theoretic Approach to Problems in Telecommunication (1996)

This paper considers two specific problems in telecommunication, namely the Terrestrial Flight Telephone System and the rerouting of international telephone calls. Both situations are modelled as coalitional games, and game theoretic techniques are used to tackle the problems. It is shown that a special class of coalitional games emerges from the situations under consideration and that the structure of the situations has theoretical implications, including the coincidence of several game theoretic solution concepts. The implications of these theoretical results for the two practical problems are discussed.
Sequence clustering and labeling for unsupervised query intent discovery (2012)

One popular form of semantic search observed in several modern search engines is to recognize query patterns that trigger instant answers or domain-specific search, producing semantically enriched search results. This often requires understanding the query intent in addition to the meaning of the query terms in order to access structured data sources. A major challenge in intent understanding is to construct a domain-dependent schema and to annotate search queries based on such a schema, a process that to date has required much manual annotation effort. We present an unsupervised method for clustering queries with similar intent and for producing a pattern consisting of a sequence of semantic concepts and/or lexical items for each intent. Furthermore, we leverage the discovered intent patterns to automatically annotate a large number of queries beyond those used in clustering. We evaluated our method on 10 selected domains, discovering over 1400 intent patterns and automatically annotating 125K (and potentially many more) queries. We found that over 90% of patterns and 80% of instance annotations tested are judged to be correct by a majority of annotators.
Si nanowire ion-sensitive field-effect transistors with a shared floating gate (2009)

Ion-sensitive field-effect transistors (ISFETs) arrayed in parallel were fabricated on a silicon-on-insulator substrate. Since the nanoscale wire channels of the ISFETs are bridged with a floating gate on which molecules are preferably immobilized, signals originating from charged materials only on the floating gate can appear and can therefore be distinguished from background noise, which leads to noise-robust sensing. Additionally, the nanoscale channels provide the ISFETs with single-electron-resolution charge sensitivity as well as a reduction in background noise induced in the wider channels used as electrical leads. These features promise the detection of a small number of molecules.
Sustained Reduction of In-Stent Neointimal Growth With the Use of a Novel Systemic Nanoparticle Paclitaxel (2002)

Although systemic nPXL reduces neointimal growth at 28 days, a single repeat dose was required for sustained neointimal suppression. Thus, this novel systemic formulation of PXL may allow adjustment of dose at the stent treatment site and prove to be a useful adjunct for the clinical prevention of in-stent restenosis.
The Genetics of Dementia with Lewy Bodies: Current Understanding and Future Directions (2018)

DLB shares risk loci with AD, in the APOE E4 allele, and with PD, in variation at GBA and SNCA. Interestingly, the GWAS suggested that DLB may also have genetic risk factors that are distinct from those in AD and PD. Although off to a slow start, recent studies have reinvigorated the field of DLB genetics and these results enable us to start to have a more complete understanding of the genetic architecture of this disease.
Combined Evidence Annotation of Transposable Elements in Genome Sequences (2005)

Transposable elements (TEs) are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1), and we found a substantially higher number of TEs (n = 6,013) than previously identified (n = 1,572). Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1). We also estimated that 518 TE copies (8.6%) are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other species in the genus Drosophila.
Boost-Buck inverter variable structure control for grid-connected photovoltaic systems (2005)

The present work describes the analysis, modeling and design of a power conditioning system for grid-connected photovoltaic (PV) systems. The designed power stage consists of a transformerless boost-buck converter. The power conditioning system's control scheme includes a variable structure controller to assure output unity power factor. To maximize the steady-state input-output energy transfer ratio a linear controller is designed out of a large-signal sampled data model of the system. The achievement of the DC-AC conversion and the efficient PV's energy extraction are validated with simulation results.
Controlled Ordering of Block Copolymer Thin Films by the Addition of Hydrophilic Nanoparticles (2007)

ADVERTISEMENT RETURN TO ISSUEPREVNoteControlled Ordering of Block Copolymer Thin Films by the Addition of Hydrophilic NanoparticlesSung Chan Park, Bumjoon J. Kim, Craig J. Hawker, Edward J. Kramer, Joona Bang, and Jeong Sook HaView Author Information Department of Chemical and Biological Engineering, Korea University, Seoul 136-701, Republic of Korea; Materials Research Laboratory, University of California, Santa Barbara, California 93106; Department of Materials, University of California, Santa Barbara, California 93106; Department of Chemical Engineering, University of California, Santa Barbara, California 93106; and Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106 Cite this: Macromolecules 2007, 40, 22, 8119–8124Publication Date (Web):October 4, 2007Publication History Received28 June 2007Revised6 August 2007Published online4 October 2007Published inissue 1 October 2007https://pubs.acs.org/doi/10.1021/ma071442zhttps://doi.org/10.1021/ma071442zbrief-reportACS PublicationsCopyright © 2007 American Chemical SocietyRequest reuse permissionsArticle Views1727Altmetric-Citations69LEARN ABOUT THESE METRICSArticle Views are the COUNTER-compliant sum of full text article downloads since November 2008 (both PDF and HTML) across all institutions and individuals. These metrics are regularly updated to reflect usage leading up to the last few days.Citations are the number of other articles citing this article, calculated by Crossref and updated daily. Find more information about Crossref citation counts.The Altmetric Attention Score is a quantitative measure of the attention that a research article has received online. Clicking on the donut icon will load a page at altmetric.com with additional details about the score and the social media presence for the given article. Find more information on the Altmetric Attention Score and how the score is calculated. Share Add toView InAdd Full Text with ReferenceAdd Description ExportRISCitationCitation and abstractCitation and referencesMore Options Share onFacebookTwitterWechatLinked InRedditEmail Other access optionsGet e-Alertsclose SUBJECTS:Copolymers,Nanoparticles,Organic compounds,Solvents,Thin films Get e-Alerts
NEPH1 defines a novel family of podocin‐interacting proteins (2002)

Mutations of NPHS1 or NPHS2, the genes encoding for the glomerular podocyte proteins nephrin and podocin, cause steroid-resistant proteinuria. In addition, mice lacking NEPH1 develop a nephrotic syndrome that resembles NPHS mutations, suggesting that all three proteins are essential for the integrity of glomerular podocytes. Podocin interacts with the C-terminal domain of nephrin and facilitates nephrin-dependent signaling. NEPH1, a member of the immunoglobulin superfamily, is structurally related to nephrin. We report now that NEPH1 belongs to a family of three closely related proteins that interact with the C-terminal domain of podocin. All three NEPH proteins share a conserved podocin-binding motif; mutation of a centrally located tyrosine residue dramatically lowers the affinity of NEPH1 for podocin. NEPH1 triggers AP-1 activation similarly to nephrin but requires the presence of Tec family kinases for efficient transactivation. We conclude that NEPH1 defines a new family of podocin-binding molecules that are potential candidates for hereditary nephrotic syndromes not linked to either NPHS1 or NPHS2.
Trigeminal ganglion innervates the auditory brainstem (2000)

A neural connection between the trigeminal ganglion and the auditory brainstem was investigated by using retrograde and anterograde tract tracing methods: iontophoretic injections of biocytin or biotinylated dextran-amine (BDA) were made into the guinea pig trigeminal ganglion, and anterograde labeling was examined in the cochlear nucleus and superior olivary complex. Terminal labeling after biocytin and BDA injections into the ganglion was found to be most dense in the marginal cell area and secondarily in the magnocellular area of the ventral cochlear nucleus (VCN). Anterograde and retrograde labeling was also seen in the shell regions of the lateral superior olivary complex and in periolivary regions. The labeling was seen in the neuropil, on neuronal somata, and in regions surrounding blood vessels. Retrograde labeling was investigated using either wheatgerm agglutinin-horseradish peroxidase (WGA-HRP), BDA, or a fluorescent tracer, iontophoretically injected into the VCN. Cells filled by retrograde labeling were found in the ophthalmic and mandibular divisions of the trigeminal ganglion. We have previously shown that these divisions project to the cochlea and middle ear, respectively. This study provides the first evidence that the trigeminal ganglion innervates the cochlear nucleus and superior olivary complex. This projection from a predominantly somatosensory ganglion may be related to integration mechanisms involving the auditory end organ and its central targets.
Estimating Body Fat from Anthropometry and Isotopic Dilution: A Four‐Country Comparison (2003)

The ability of BMI to adequately predict BF and the additional predictivity of anthropometric measures varied widely across the samples, making its uniform use as a proxy for BF in youths from different countries questionable.
A System for Induction of Oblique Decision Trees (1994)

This article describes a new system for induction ofoblique decision trees. This system, OC1, combines deterministic hill-climbing with two forms of randomization to find a goodoblique split (in the form of a hyperplane) at each node of a decisiontree. Oblique decision tree methods are tuned especially for domains in which the attributes are numeric, although they can be adapted to symbolic or mixed symbolic/numeric attributes. We presentextensive empirical studies, using both real and artificial data, thatanalyze OC1's ability to construct oblique trees that are smaller and more accurate than their axis-parallel counterparts. We also examinethe benefits of randomization for the construction of oblique decisiontrees.
Molecular Mechanisms and Potential Therapeutical Targets in Huntington's Disease (2010)

Huntington's disease (HD) is a neurodegenerative disorder caused by a CAG repeat expansion in the gene encoding for huntingtin protein. A lot has been learned about this disease since its first description in 1872 and the identification of its causative gene and mutation in 1993. We now know that the disease is characterized by several molecular and cellular abnormalities whose precise timing and relative roles in pathogenesis have yet to be understood. HD is triggered by the mutant protein, and both gain-of-function (of the mutant protein) and loss-of-function (of the normal protein) mechanisms are involved. Here we review the data that describe the emergence of the ancient huntingtin gene and of the polyglutamine trait during the last 800 million years of evolution. We focus on the known functions of wild-type huntingtin that are fundamental for the survival and functioning of the brain neurons that predominantly degenerate in HD. We summarize data indicating how the loss of these beneficial activities reduces the ability of these neurons to survive. We also review the different mechanisms by which the mutation in huntingtin causes toxicity. This may arise both from cell-autonomous processes and dysfunction of neuronal circuitries. We then focus on novel therapeutical targets and pathways and on the attractive option to counteract HD at its primary source, i.e., by blocking the production of the mutant protein. Strategies and technologies used to screen for candidate HD biomarkers and their potential application are presented. Furthermore, we discuss the opportunities offered by intracerebral cell transplantation and the likely need for these multiple routes into therapies to converge at some point as, ideally, one would wish to stop the disease process and, at the same time, possibly replace the damaged neurons.
An optical network unit for WDM access networks with downstream DPSK and upstream remodulated OOK data using injection-locked FP laser (2003)

We investigate the use of optical differential phase-shift keying (DPSK) as the downstream modulation format in a low-cost upstream data remodulation scheme for a wavelength-division multiplexing (WDM)-based passive optical network. A 2.5-Gb/s upstream data transmitter is realized by directly modulating a Fabry-Perot (FP) laser, injection-locked with a 10-Gb/s downstream optical DPSK signal. A simple polarization-offset technique is proposed to largely minimize the induced power penalty.
Corneal Punctate Staining With Latanoprost, Bimatoprost, and Travoprost in Healthy Subjects (2003)

This study suggests that, in healthy subjects after short-term treatment, latanoprost, bimatoprost, and travoprost demonstrate generally similar ocular surface epithelial staining characteristics.
Quilt: a collaborative tool for cooperative writing (1988)

Quilt is a computer-based tool for collaborative writing, which provides annotation, messaging, computer conferencing, and notification facilities to support communication and information sharing among the collaborators on a document. In addition, extensible sets of social roles and communication types are used to provide views of a document tailored to individual collaborators or to other users of the document based upon their position in a permission hierarchy. This paper describes the rationale for and design of Quilt.
CpG methylation of viral DNA in EBV‐associated tumours (1990)

In EBV-immortalized lymphoblastoid cell lines (LCLs) a small number of "latent" proteins are expressed. These are the EBV nuclear antigens, EBNAs 1-6, and a latent membrane protein, LMP. We have investigated the expression of these proteins in a variety of EBV-associated tumours and cell lines. Whereas transplant and B-cell lymphomas from cotton-top tamarins appear to express the full range of antigens found in LCLs, we and others have found that in Burkitt's lymphomas (BL) and a nasopharyngeal carcinoma (NPC) isolate, EBNA expression is restricted to EBNA-I. (In NPC, but not in BL, LMP may also be expressed). In order to ask what restricts the expression of EBNA 2-6 in NPC and BL cells it seemed reasonable to consider the possibility that the DNA sequences normally regulating expression of these antigens could be chemically modified. In this analysis, a tight inverse correlation between methylation of CpG dinucleotides in the 5' flanking region of the EBNA-2 gene and the expression of EBNAs 2-6 has been revealed. In the NPC tumour, CpG methylation within the gene is also observed, as is specific methylation over the EBNA-I region I and II binding sites (in oriP). The significance of these observations is considered.